Starting phenix.real_space_refine on Sat Aug 23 05:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qki_18463/08_2025/8qki_18463_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qki_18463/08_2025/8qki_18463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qki_18463/08_2025/8qki_18463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qki_18463/08_2025/8qki_18463.map" model { file = "/net/cci-nas-00/data/ceres_data/8qki_18463/08_2025/8qki_18463_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qki_18463/08_2025/8qki_18463_neut.cif" } resolution = 3.46 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= 0.000 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6780 2.51 5 N 1680 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1670 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.45, per 1000 atoms: 0.14 Number of scatterers: 10188 At special positions: 0 Unit cell: (98.15, 101.4, 91.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 1638 8.00 N 1680 7.00 C 6780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 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: 0.81 Conformation dependent library (CDL) restraints added in 312.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 75.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 42 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 108 Proline residue: A 87 - end of helix removed outlier: 3.760A pdb=" N ARG A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 157 Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 42 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 108 Proline residue: B 87 - end of helix removed outlier: 3.760A pdb=" N ARG B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 157 Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 42 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 108 Proline residue: C 87 - end of helix removed outlier: 3.760A pdb=" N ARG C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 157 Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 42 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 108 Proline residue: D 87 - end of helix removed outlier: 3.761A pdb=" N ARG D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 157 Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 42 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 108 Proline residue: E 87 - end of helix removed outlier: 3.760A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 157 Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 42 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 108 Proline residue: F 87 - end of helix removed outlier: 3.760A pdb=" N ARG F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 157 Processing helix chain 'F' and resid 183 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 780 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3030 1.35 - 1.46: 2697 1.46 - 1.58: 4615 1.58 - 1.70: 2 1.70 - 1.82: 132 Bond restraints: 10476 Sorted by residual: bond pdb=" C6 CLR E 501 " pdb=" C7 CLR E 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" C6 CLR D 501 " pdb=" C7 CLR D 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C6 CLR F 501 " pdb=" C7 CLR F 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" C6 CLR A 501 " pdb=" C7 CLR A 501 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C6 CLR B 501 " pdb=" C7 CLR B 501 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 13804 1.66 - 3.31: 332 3.31 - 4.97: 106 4.97 - 6.63: 44 6.63 - 8.28: 18 Bond angle restraints: 14304 Sorted by residual: angle pdb=" CB GLN A 98 " pdb=" CG GLN A 98 " pdb=" CD GLN A 98 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.70e+00 3.46e-01 7.72e+00 angle pdb=" CB GLN D 98 " pdb=" CG GLN D 98 " pdb=" CD GLN D 98 " ideal model delta sigma weight residual 112.60 117.31 -4.71 1.70e+00 3.46e-01 7.67e+00 angle pdb=" CB GLN C 98 " pdb=" CG GLN C 98 " pdb=" CD GLN C 98 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.70e+00 3.46e-01 7.64e+00 angle pdb=" C22 CLR C 501 " pdb=" C23 CLR C 501 " pdb=" C24 CLR C 501 " ideal model delta sigma weight residual 111.95 103.67 8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB GLN E 98 " pdb=" CG GLN E 98 " pdb=" CD GLN E 98 " ideal model delta sigma weight residual 112.60 117.28 -4.68 1.70e+00 3.46e-01 7.57e+00 ... (remaining 14299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 5503 11.70 - 23.40: 545 23.40 - 35.11: 240 35.11 - 46.81: 96 46.81 - 58.51: 36 Dihedral angle restraints: 6420 sinusoidal: 2748 harmonic: 3672 Sorted by residual: dihedral pdb=" CA ASP B 46 " pdb=" C ASP B 46 " pdb=" N GLU B 47 " pdb=" CA GLU B 47 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP F 46 " pdb=" C ASP F 46 " pdb=" N GLU F 47 " pdb=" CA GLU F 47 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP A 46 " pdb=" C ASP A 46 " pdb=" N GLU A 47 " pdb=" CA GLU A 47 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1583 0.073 - 0.147: 97 0.147 - 0.220: 0 0.220 - 0.293: 7 0.293 - 0.367: 17 Chirality restraints: 1704 Sorted by residual: chirality pdb=" C17 CLR B 501 " pdb=" C13 CLR B 501 " pdb=" C16 CLR B 501 " pdb=" C20 CLR B 501 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C17 CLR D 501 " pdb=" C13 CLR D 501 " pdb=" C16 CLR D 501 " pdb=" C20 CLR D 501 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C17 CLR E 501 " pdb=" C13 CLR E 501 " pdb=" C16 CLR E 501 " pdb=" C20 CLR E 501 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1701 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 211 " -0.005 2.00e-02 2.50e+03 7.56e-03 1.14e+00 pdb=" CG TYR B 211 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 211 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 211 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 211 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 211 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 211 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 211 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 211 " -0.004 2.00e-02 2.50e+03 7.51e-03 1.13e+00 pdb=" CG TYR A 211 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 211 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 211 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 211 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 211 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 211 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 211 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 211 " 0.004 2.00e-02 2.50e+03 7.51e-03 1.13e+00 pdb=" CG TYR E 211 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 211 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 211 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 211 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 211 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 211 " -0.001 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 45 2.64 - 3.20: 9475 3.20 - 3.77: 16878 3.77 - 4.33: 20935 4.33 - 4.90: 35726 Nonbonded interactions: 83059 Sorted by model distance: nonbonded pdb=" OG SER A 182 " pdb=" NZ LYS F 48 " model vdw 2.071 3.120 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 157 " model vdw 2.199 3.040 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 157 " model vdw 2.199 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 157 " model vdw 2.199 3.040 nonbonded pdb=" O ILE E 71 " pdb=" OH TYR E 157 " model vdw 2.199 3.040 ... (remaining 83054 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.890 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.004 0.050 10494 Z= 0.185 Angle : 0.751 8.284 14340 Z= 0.354 Chirality : 0.052 0.367 1704 Planarity : 0.002 0.014 1674 Dihedral : 12.595 58.509 3978 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.54 % Allowed : 3.76 % Favored : 95.70 % 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 aren not related in a simple way. whole: 2.14 (0.24), residues: 1218 helix: 2.50 (0.16), residues: 882 sheet: -0.88 (0.47), residues: 102 loop : -1.88 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 142 TYR 0.018 0.002 TYR B 211 PHE 0.006 0.001 PHE B 149 TRP 0.004 0.001 TRP E 132 HIS 0.005 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00377 (10476) covalent geometry : angle 0.75204 (14304) SS BOND : bond 0.00136 ( 18) SS BOND : angle 0.20668 ( 36) hydrogen bonds : bond 0.09225 ( 780) hydrogen bonds : angle 4.40385 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 314 time to evaluate : 0.341 Fit side-chains REVERT: A 13 VAL cc_start: 0.9149 (m) cc_final: 0.8898 (p) REVERT: A 34 MET cc_start: 0.7579 (mmm) cc_final: 0.7370 (mmt) REVERT: B 66 ASP cc_start: 0.7978 (t0) cc_final: 0.7717 (t0) REVERT: B 150 MET cc_start: 0.7869 (mmp) cc_final: 0.6999 (tmm) REVERT: C 34 MET cc_start: 0.7996 (mmm) cc_final: 0.7641 (mmt) REVERT: C 54 ASN cc_start: 0.8937 (t0) cc_final: 0.8634 (t0) REVERT: C 66 ASP cc_start: 0.7819 (t0) cc_final: 0.7543 (t0) REVERT: C 150 MET cc_start: 0.7649 (mmp) cc_final: 0.6819 (tmm) REVERT: D 54 ASN cc_start: 0.8893 (t0) cc_final: 0.8609 (t0) REVERT: D 66 ASP cc_start: 0.7719 (t0) cc_final: 0.7501 (t0) REVERT: D 150 MET cc_start: 0.7655 (mmp) cc_final: 0.6816 (tmm) REVERT: E 54 ASN cc_start: 0.8943 (t0) cc_final: 0.8601 (t0) REVERT: E 66 ASP cc_start: 0.7866 (t0) cc_final: 0.7598 (t0) REVERT: E 150 MET cc_start: 0.7793 (mmp) cc_final: 0.6954 (tmm) REVERT: F 34 MET cc_start: 0.8005 (mmm) cc_final: 0.7698 (mmt) REVERT: F 54 ASN cc_start: 0.8975 (t0) cc_final: 0.8654 (t0) REVERT: F 66 ASP cc_start: 0.7668 (t0) cc_final: 0.7443 (t0) REVERT: F 150 MET cc_start: 0.7706 (mmp) cc_final: 0.6814 (tmm) outliers start: 6 outliers final: 0 residues processed: 315 average time/residue: 0.0850 time to fit residues: 38.1028 Evaluate side-chains 259 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.062220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.053065 restraints weight = 32231.266| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.82 r_work: 0.2759 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10494 Z= 0.255 Angle : 0.665 6.430 14340 Z= 0.338 Chirality : 0.042 0.138 1704 Planarity : 0.004 0.026 1674 Dihedral : 6.230 59.687 1746 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.15 % Allowed : 13.44 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.24), residues: 1218 helix: 3.12 (0.15), residues: 894 sheet: -0.66 (0.49), residues: 102 loop : -1.57 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 142 TYR 0.013 0.002 TYR A 157 PHE 0.012 0.002 PHE D 149 TRP 0.015 0.001 TRP A 24 HIS 0.005 0.001 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00576 (10476) covalent geometry : angle 0.66592 (14304) SS BOND : bond 0.00280 ( 18) SS BOND : angle 0.43908 ( 36) hydrogen bonds : bond 0.03367 ( 780) hydrogen bonds : angle 3.26287 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.363 Fit side-chains REVERT: A 123 HIS cc_start: 0.8342 (t70) cc_final: 0.8027 (t70) REVERT: A 146 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8894 (tp30) REVERT: B 144 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8937 (mm) REVERT: C 54 ASN cc_start: 0.9339 (t0) cc_final: 0.9006 (t0) REVERT: C 98 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8559 (mp10) REVERT: C 102 GLU cc_start: 0.9016 (tp30) cc_final: 0.8602 (mm-30) REVERT: D 205 ASN cc_start: 0.9064 (m-40) cc_final: 0.8702 (m110) REVERT: E 144 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8951 (mm) REVERT: F 98 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8550 (mp10) outliers start: 24 outliers final: 16 residues processed: 229 average time/residue: 0.1013 time to fit residues: 32.2413 Evaluate side-chains 205 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 94 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN D 54 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 94 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054708 restraints weight = 31722.550| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.83 r_work: 0.2799 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10494 Z= 0.154 Angle : 0.541 5.579 14340 Z= 0.271 Chirality : 0.039 0.146 1704 Planarity : 0.003 0.020 1674 Dihedral : 5.669 60.000 1746 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.96 % Allowed : 13.89 % Favored : 83.15 % 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 aren not related in a simple way. whole: 3.34 (0.24), residues: 1218 helix: 3.30 (0.15), residues: 894 sheet: -0.33 (0.53), residues: 102 loop : -1.46 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.007 0.001 TYR E 151 PHE 0.008 0.001 PHE B 149 TRP 0.008 0.001 TRP A 44 HIS 0.003 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00350 (10476) covalent geometry : angle 0.54132 (14304) SS BOND : bond 0.00188 ( 18) SS BOND : angle 0.25482 ( 36) hydrogen bonds : bond 0.03008 ( 780) hydrogen bonds : angle 3.15084 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.341 Fit side-chains REVERT: A 48 LYS cc_start: 0.9240 (tppp) cc_final: 0.9029 (mmmm) REVERT: A 123 HIS cc_start: 0.8369 (t70) cc_final: 0.7837 (t70) REVERT: B 57 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8632 (tm-30) REVERT: C 98 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8603 (mp10) REVERT: C 102 GLU cc_start: 0.9058 (tp30) cc_final: 0.8628 (mm-30) REVERT: C 144 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9000 (mm) REVERT: D 48 LYS cc_start: 0.7805 (mptt) cc_final: 0.7558 (mmmm) REVERT: D 57 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8646 (tm-30) REVERT: D 99 GLN cc_start: 0.9198 (tt0) cc_final: 0.8976 (mt0) REVERT: D 102 GLU cc_start: 0.9075 (tp30) cc_final: 0.8602 (mm-30) REVERT: D 146 GLU cc_start: 0.9209 (mm-30) cc_final: 0.9005 (tp30) REVERT: E 57 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8574 (tm-30) REVERT: F 57 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8611 (tm-30) REVERT: F 98 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8582 (mp10) REVERT: F 102 GLU cc_start: 0.9004 (tp30) cc_final: 0.8593 (mm-30) outliers start: 33 outliers final: 25 residues processed: 230 average time/residue: 0.0912 time to fit residues: 29.4040 Evaluate side-chains 221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.052908 restraints weight = 31941.906| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.74 r_work: 0.2748 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10494 Z= 0.224 Angle : 0.574 5.603 14340 Z= 0.293 Chirality : 0.041 0.133 1704 Planarity : 0.003 0.018 1674 Dihedral : 6.092 57.385 1746 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.66 % Allowed : 13.53 % Favored : 81.81 % 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 aren not related in a simple way. whole: 3.34 (0.24), residues: 1218 helix: 3.29 (0.15), residues: 900 sheet: -0.49 (0.52), residues: 102 loop : -1.44 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.012 0.001 TYR D 151 PHE 0.010 0.001 PHE C 149 TRP 0.009 0.001 TRP F 24 HIS 0.003 0.001 HIS E 16 Details of bonding type rmsd covalent geometry : bond 0.00497 (10476) covalent geometry : angle 0.57493 (14304) SS BOND : bond 0.00287 ( 18) SS BOND : angle 0.27160 ( 36) hydrogen bonds : bond 0.03196 ( 780) hydrogen bonds : angle 3.22909 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.445 Fit side-chains REVERT: A 48 LYS cc_start: 0.9197 (tppp) cc_final: 0.8981 (mmmm) REVERT: A 94 HIS cc_start: 0.9093 (t70) cc_final: 0.8662 (t-90) REVERT: A 123 HIS cc_start: 0.8306 (t70) cc_final: 0.7931 (t70) REVERT: B 144 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9127 (mm) REVERT: C 57 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8687 (tm-30) REVERT: C 102 GLU cc_start: 0.9095 (tp30) cc_final: 0.8685 (mm-30) REVERT: D 57 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8594 (tm-30) REVERT: D 99 GLN cc_start: 0.9176 (tt0) cc_final: 0.8928 (mt0) REVERT: D 102 GLU cc_start: 0.9076 (tp30) cc_final: 0.8687 (mm-30) REVERT: D 146 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8933 (tp30) REVERT: E 57 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8566 (tm-30) REVERT: E 99 GLN cc_start: 0.9096 (mt0) cc_final: 0.8893 (mt0) REVERT: E 144 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9160 (mm) REVERT: F 57 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8591 (tm-30) REVERT: F 102 GLU cc_start: 0.9046 (tp30) cc_final: 0.8639 (mm-30) outliers start: 52 outliers final: 31 residues processed: 249 average time/residue: 0.1069 time to fit residues: 37.3805 Evaluate side-chains 233 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 94 HIS B 98 GLN B 123 HIS C 94 HIS ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS F 94 HIS ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.064227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.054908 restraints weight = 31133.084| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.82 r_work: 0.2797 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10494 Z= 0.131 Angle : 0.549 6.570 14340 Z= 0.280 Chirality : 0.038 0.125 1704 Planarity : 0.003 0.017 1674 Dihedral : 5.811 57.786 1746 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.33 % Allowed : 15.50 % Favored : 82.17 % 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 aren not related in a simple way. whole: 3.50 (0.24), residues: 1218 helix: 3.39 (0.16), residues: 900 sheet: -0.68 (0.49), residues: 102 loop : -1.13 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.007 0.001 TYR C 65 PHE 0.007 0.001 PHE A 31 TRP 0.009 0.001 TRP E 44 HIS 0.003 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00289 (10476) covalent geometry : angle 0.54936 (14304) SS BOND : bond 0.00143 ( 18) SS BOND : angle 0.22937 ( 36) hydrogen bonds : bond 0.02832 ( 780) hydrogen bonds : angle 3.09692 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9166 (tppp) cc_final: 0.8931 (mmtt) REVERT: A 94 HIS cc_start: 0.9077 (t70) cc_final: 0.8595 (t-90) REVERT: A 123 HIS cc_start: 0.8275 (t70) cc_final: 0.7911 (t70) REVERT: B 144 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9031 (mm) REVERT: C 47 GLU cc_start: 0.8286 (tp30) cc_final: 0.8019 (tp30) REVERT: C 57 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8450 (tm-30) REVERT: C 102 GLU cc_start: 0.9143 (tp30) cc_final: 0.8783 (mm-30) REVERT: D 94 HIS cc_start: 0.8978 (t-90) cc_final: 0.8731 (t-90) REVERT: D 102 GLU cc_start: 0.9112 (tp30) cc_final: 0.8696 (mm-30) REVERT: D 124 LYS cc_start: 0.9278 (mmmm) cc_final: 0.9041 (mmmm) REVERT: D 146 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8891 (tp30) REVERT: E 47 GLU cc_start: 0.8366 (tp30) cc_final: 0.8029 (tp30) REVERT: E 144 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9040 (mm) REVERT: F 102 GLU cc_start: 0.9088 (tp30) cc_final: 0.8723 (mm-30) REVERT: F 144 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9136 (mm) outliers start: 26 outliers final: 18 residues processed: 239 average time/residue: 0.0955 time to fit residues: 32.0925 Evaluate side-chains 227 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN C 94 HIS ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.063124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053863 restraints weight = 31791.333| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.75 r_work: 0.2771 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10494 Z= 0.171 Angle : 0.570 7.131 14340 Z= 0.291 Chirality : 0.039 0.123 1704 Planarity : 0.003 0.022 1674 Dihedral : 5.815 54.964 1746 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.87 % Allowed : 15.05 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.24), residues: 1218 helix: 3.40 (0.16), residues: 888 sheet: -0.79 (0.48), residues: 102 loop : -1.08 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 183 TYR 0.010 0.001 TYR F 65 PHE 0.009 0.001 PHE A 149 TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00378 (10476) covalent geometry : angle 0.57101 (14304) SS BOND : bond 0.00197 ( 18) SS BOND : angle 0.22641 ( 36) hydrogen bonds : bond 0.02896 ( 780) hydrogen bonds : angle 3.09100 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9147 (tppp) cc_final: 0.8916 (mmtt) REVERT: A 94 HIS cc_start: 0.9092 (t70) cc_final: 0.8600 (t-90) REVERT: A 123 HIS cc_start: 0.8299 (t70) cc_final: 0.7950 (t70) REVERT: B 47 GLU cc_start: 0.8320 (tp30) cc_final: 0.7950 (tp30) REVERT: B 57 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 102 GLU cc_start: 0.9163 (tp30) cc_final: 0.8896 (mm-30) REVERT: B 144 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9115 (mm) REVERT: C 57 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8484 (tm-30) REVERT: C 94 HIS cc_start: 0.9069 (t70) cc_final: 0.8843 (t-90) REVERT: C 102 GLU cc_start: 0.9148 (tp30) cc_final: 0.8783 (mm-30) REVERT: D 47 GLU cc_start: 0.8121 (tp30) cc_final: 0.7742 (tp30) REVERT: D 57 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8377 (tm-30) REVERT: D 94 HIS cc_start: 0.9009 (t-90) cc_final: 0.8793 (t-90) REVERT: D 102 GLU cc_start: 0.9131 (tp30) cc_final: 0.8721 (mm-30) REVERT: D 124 LYS cc_start: 0.9282 (mmmm) cc_final: 0.9049 (mmmm) REVERT: E 57 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8381 (tm-30) REVERT: E 98 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8645 (tp40) REVERT: E 102 GLU cc_start: 0.9150 (tp30) cc_final: 0.8897 (mm-30) REVERT: E 144 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9121 (mm) REVERT: F 47 GLU cc_start: 0.8231 (tp30) cc_final: 0.8027 (tp30) REVERT: F 57 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8425 (tm-30) REVERT: F 94 HIS cc_start: 0.9022 (t70) cc_final: 0.8714 (t-90) REVERT: F 102 GLU cc_start: 0.9101 (tp30) cc_final: 0.8737 (mm-30) outliers start: 32 outliers final: 24 residues processed: 233 average time/residue: 0.0968 time to fit residues: 31.3078 Evaluate side-chains 229 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN B 123 HIS C 98 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056232 restraints weight = 31172.534| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.83 r_work: 0.2828 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10494 Z= 0.117 Angle : 0.567 7.739 14340 Z= 0.285 Chirality : 0.037 0.159 1704 Planarity : 0.003 0.020 1674 Dihedral : 5.452 54.886 1746 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.79 % Allowed : 16.22 % Favored : 81.99 % 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 aren not related in a simple way. whole: 3.62 (0.24), residues: 1218 helix: 3.53 (0.16), residues: 888 sheet: -0.82 (0.48), residues: 102 loop : -0.99 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.008 0.001 TYR E 65 PHE 0.007 0.001 PHE D 149 TRP 0.010 0.001 TRP C 44 HIS 0.003 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00251 (10476) covalent geometry : angle 0.56790 (14304) SS BOND : bond 0.00096 ( 18) SS BOND : angle 0.20246 ( 36) hydrogen bonds : bond 0.02606 ( 780) hydrogen bonds : angle 3.02693 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.405 Fit side-chains REVERT: A 94 HIS cc_start: 0.9065 (t70) cc_final: 0.8731 (t-90) REVERT: A 123 HIS cc_start: 0.8276 (t70) cc_final: 0.7943 (t70) REVERT: B 144 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9026 (mm) REVERT: C 47 GLU cc_start: 0.8352 (tp30) cc_final: 0.8147 (tp30) REVERT: C 57 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 102 GLU cc_start: 0.9181 (tp30) cc_final: 0.8846 (mm-30) REVERT: C 146 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8938 (tp30) REVERT: D 94 HIS cc_start: 0.8986 (t-90) cc_final: 0.8762 (t-90) REVERT: D 102 GLU cc_start: 0.9158 (tp30) cc_final: 0.8767 (mm-30) REVERT: D 124 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9074 (mmmm) REVERT: D 146 GLU cc_start: 0.8857 (tp30) cc_final: 0.8454 (tp30) REVERT: E 144 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9020 (mm) REVERT: F 102 GLU cc_start: 0.9133 (tp30) cc_final: 0.8781 (mm-30) REVERT: F 105 MET cc_start: 0.8477 (mtt) cc_final: 0.8263 (mtm) REVERT: F 144 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9057 (mm) outliers start: 20 outliers final: 12 residues processed: 227 average time/residue: 0.0977 time to fit residues: 31.0990 Evaluate side-chains 211 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS F 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.056483 restraints weight = 30994.066| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.81 r_work: 0.2845 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10494 Z= 0.117 Angle : 0.591 7.958 14340 Z= 0.297 Chirality : 0.037 0.174 1704 Planarity : 0.003 0.032 1674 Dihedral : 5.361 54.533 1746 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.52 % Allowed : 17.56 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.24), residues: 1218 helix: 3.58 (0.16), residues: 888 sheet: -0.87 (0.47), residues: 102 loop : -1.00 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 32 TYR 0.009 0.001 TYR A 65 PHE 0.007 0.001 PHE D 149 TRP 0.012 0.001 TRP E 44 HIS 0.003 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00250 (10476) covalent geometry : angle 0.59157 (14304) SS BOND : bond 0.00097 ( 18) SS BOND : angle 0.21131 ( 36) hydrogen bonds : bond 0.02625 ( 780) hydrogen bonds : angle 2.98704 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.435 Fit side-chains REVERT: A 94 HIS cc_start: 0.9046 (t70) cc_final: 0.8717 (t-90) REVERT: A 123 HIS cc_start: 0.8262 (t70) cc_final: 0.7956 (t70) REVERT: B 57 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 144 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9047 (mm) REVERT: C 47 GLU cc_start: 0.8198 (tp30) cc_final: 0.7965 (tp30) REVERT: C 57 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 94 HIS cc_start: 0.9022 (t70) cc_final: 0.8579 (t-90) REVERT: C 102 GLU cc_start: 0.9188 (tp30) cc_final: 0.8870 (mm-30) REVERT: C 144 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9107 (mm) REVERT: C 146 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8780 (tp30) REVERT: D 57 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8226 (tm-30) REVERT: D 94 HIS cc_start: 0.8948 (t-90) cc_final: 0.8740 (t-90) REVERT: D 102 GLU cc_start: 0.9143 (tp30) cc_final: 0.8756 (mm-30) REVERT: D 124 LYS cc_start: 0.9291 (mmmm) cc_final: 0.9086 (mmmm) REVERT: E 47 GLU cc_start: 0.8175 (tp30) cc_final: 0.7919 (tm-30) REVERT: E 57 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8210 (tm-30) REVERT: E 144 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9045 (mm) REVERT: F 47 GLU cc_start: 0.8220 (tp30) cc_final: 0.8018 (tp30) REVERT: F 57 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8308 (tm-30) REVERT: F 94 HIS cc_start: 0.8981 (t70) cc_final: 0.8463 (t-90) REVERT: F 102 GLU cc_start: 0.9136 (tp30) cc_final: 0.8799 (mm-30) REVERT: F 105 MET cc_start: 0.8471 (mtt) cc_final: 0.8259 (mtm) REVERT: F 144 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9131 (mm) outliers start: 17 outliers final: 11 residues processed: 223 average time/residue: 0.0852 time to fit residues: 26.7799 Evaluate side-chains 211 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN C 98 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 98 GLN F 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057232 restraints weight = 30858.774| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.82 r_work: 0.2864 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10494 Z= 0.116 Angle : 0.598 9.526 14340 Z= 0.297 Chirality : 0.037 0.121 1704 Planarity : 0.003 0.026 1674 Dihedral : 5.263 55.221 1746 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 17.29 % Favored : 81.45 % 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 aren not related in a simple way. whole: 3.71 (0.24), residues: 1218 helix: 3.61 (0.16), residues: 888 sheet: -0.89 (0.48), residues: 102 loop : -0.95 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 32 TYR 0.008 0.001 TYR C 171 PHE 0.007 0.001 PHE F 31 TRP 0.013 0.001 TRP F 44 HIS 0.003 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00248 (10476) covalent geometry : angle 0.59866 (14304) SS BOND : bond 0.00089 ( 18) SS BOND : angle 0.26288 ( 36) hydrogen bonds : bond 0.02523 ( 780) hydrogen bonds : angle 2.96817 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 94 HIS cc_start: 0.9035 (t70) cc_final: 0.8705 (t-90) REVERT: B 57 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 144 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9033 (mm) REVERT: C 57 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 94 HIS cc_start: 0.9029 (t70) cc_final: 0.8499 (t-90) REVERT: C 102 GLU cc_start: 0.9186 (tp30) cc_final: 0.8868 (mm-30) REVERT: C 144 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9047 (mm) REVERT: D 57 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8190 (tm-30) REVERT: D 94 HIS cc_start: 0.8970 (t-90) cc_final: 0.8605 (t-90) REVERT: D 102 GLU cc_start: 0.9171 (tp30) cc_final: 0.8770 (mm-30) REVERT: D 105 MET cc_start: 0.8326 (mtt) cc_final: 0.8006 (mtp) REVERT: D 124 LYS cc_start: 0.9306 (mmmm) cc_final: 0.9103 (mmmm) REVERT: E 57 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8133 (tm-30) REVERT: E 144 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9027 (mm) REVERT: F 57 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8279 (tm-30) REVERT: F 94 HIS cc_start: 0.8972 (t70) cc_final: 0.8470 (t-90) REVERT: F 102 GLU cc_start: 0.9131 (tp30) cc_final: 0.8796 (mm-30) REVERT: F 105 MET cc_start: 0.8499 (mtt) cc_final: 0.8286 (mtm) REVERT: F 144 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9035 (mm) outliers start: 14 outliers final: 9 residues processed: 225 average time/residue: 0.0895 time to fit residues: 28.4007 Evaluate side-chains 208 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 98 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN C 98 GLN D 94 HIS D 98 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 98 GLN F 67 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.054951 restraints weight = 31133.755| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.84 r_work: 0.2807 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10494 Z= 0.152 Angle : 0.637 11.291 14340 Z= 0.317 Chirality : 0.038 0.128 1704 Planarity : 0.003 0.023 1674 Dihedral : 5.529 58.824 1746 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.43 % Allowed : 18.64 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.24), residues: 1218 helix: 3.56 (0.16), residues: 888 sheet: -0.88 (0.47), residues: 102 loop : -0.94 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 32 TYR 0.032 0.001 TYR D 7 PHE 0.009 0.001 PHE C 149 TRP 0.013 0.001 TRP E 44 HIS 0.002 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00337 (10476) covalent geometry : angle 0.63730 (14304) SS BOND : bond 0.00166 ( 18) SS BOND : angle 0.34642 ( 36) hydrogen bonds : bond 0.02761 ( 780) hydrogen bonds : angle 3.02504 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 94 HIS cc_start: 0.9086 (t70) cc_final: 0.8745 (t-90) REVERT: A 123 HIS cc_start: 0.8269 (t70) cc_final: 0.7960 (t70) REVERT: B 57 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 144 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9045 (mm) REVERT: C 57 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 94 HIS cc_start: 0.9002 (t70) cc_final: 0.8490 (t-90) REVERT: C 102 GLU cc_start: 0.9201 (tp30) cc_final: 0.8884 (mm-30) REVERT: D 57 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 102 GLU cc_start: 0.9165 (tp30) cc_final: 0.8774 (mm-30) REVERT: D 105 MET cc_start: 0.8340 (mtt) cc_final: 0.8017 (mtp) REVERT: D 124 LYS cc_start: 0.9304 (mmmm) cc_final: 0.9088 (mmmm) REVERT: E 57 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8183 (tm-30) REVERT: E 144 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9036 (mm) REVERT: F 57 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8298 (tm-30) REVERT: F 94 HIS cc_start: 0.8996 (t70) cc_final: 0.8628 (t-90) REVERT: F 102 GLU cc_start: 0.9146 (tp30) cc_final: 0.8810 (mm-30) REVERT: F 105 MET cc_start: 0.8487 (mtt) cc_final: 0.8279 (mtm) outliers start: 16 outliers final: 14 residues processed: 219 average time/residue: 0.0860 time to fit residues: 27.0212 Evaluate side-chains 217 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 98 GLN C 98 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 98 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.055667 restraints weight = 31231.680| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.97 r_work: 0.2844 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10494 Z= 0.128 Angle : 0.640 10.592 14340 Z= 0.318 Chirality : 0.037 0.135 1704 Planarity : 0.003 0.028 1674 Dihedral : 5.396 57.670 1746 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.34 % Allowed : 18.64 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.75 (0.24), residues: 1218 helix: 3.57 (0.16), residues: 900 sheet: -0.84 (0.47), residues: 102 loop : -0.92 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 32 TYR 0.029 0.001 TYR D 7 PHE 0.008 0.001 PHE A 31 TRP 0.011 0.001 TRP F 44 HIS 0.003 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00281 (10476) covalent geometry : angle 0.64039 (14304) SS BOND : bond 0.00110 ( 18) SS BOND : angle 0.30466 ( 36) hydrogen bonds : bond 0.02584 ( 780) hydrogen bonds : angle 3.02134 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.02 seconds wall clock time: 31 minutes 50.56 seconds (1910.56 seconds total)