Starting phenix.real_space_refine on Thu Mar 6 07:52:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ic3_4452/03_2025/6ic3_4452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ic3_4452/03_2025/6ic3_4452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2025/6ic3_4452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2025/6ic3_4452.map" model { file = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2025/6ic3_4452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2025/6ic3_4452.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 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 16 5.16 5 C 3400 2.51 5 N 968 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5472 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 2.43, per 1000 atoms: 0.44 Number of scatterers: 5472 At special positions: 0 Unit cell: (79.116, 92.649, 56.214, 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 16 16.00 O 1088 8.00 N 968 7.00 C 3400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.02 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: 1.17 Conformation dependent library (CDL) restraints added in 681.6 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 8.197A pdb=" N ARG A 25 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ARG B 25 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ARG C 25 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ARG D 25 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG E 25 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ARG F 25 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG G 25 " --> pdb=" O SER H 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.231A pdb=" N LEU A 47 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 47 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 47 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 47 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU E 47 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 47 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU G 47 " --> pdb=" O LEU H 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.628A pdb=" N GLU A 82 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B 82 " --> pdb=" O ASP C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.819A pdb=" N ALA A 94 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 94 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA C 94 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA D 94 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA E 94 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA F 94 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA G 94 " --> pdb=" O THR H 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.641A pdb=" N GLU D 82 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU E 82 " --> pdb=" O ASP F 83 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU F 82 " --> pdb=" O ASP G 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 33 through 35 32 hydrogen bonds defined for protein. 96 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: 1.29 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1755 1.33 - 1.45: 885 1.45 - 1.56: 2944 1.56 - 1.68: 0 1.68 - 1.79: 16 Bond restraints: 5600 Sorted by residual: bond pdb=" CB TYR H 88 " pdb=" CG TYR H 88 " ideal model delta sigma weight residual 1.512 1.476 0.036 2.20e-02 2.07e+03 2.61e+00 bond pdb=" CB TYR C 88 " pdb=" CG TYR C 88 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.60e+00 bond pdb=" CB TYR E 88 " pdb=" CG TYR E 88 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.58e+00 bond pdb=" CB TYR F 88 " pdb=" CG TYR F 88 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.57e+00 bond pdb=" CB TYR A 88 " pdb=" CG TYR A 88 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.55e+00 ... (remaining 5595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 6823 1.79 - 3.58: 589 3.58 - 5.37: 132 5.37 - 7.17: 24 7.17 - 8.96: 32 Bond angle restraints: 7600 Sorted by residual: angle pdb=" N PHE C 40 " pdb=" CA PHE C 40 " pdb=" C PHE C 40 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N PHE F 40 " pdb=" CA PHE F 40 " pdb=" C PHE F 40 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N PHE G 40 " pdb=" CA PHE G 40 " pdb=" C PHE G 40 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N PHE H 40 " pdb=" CA PHE H 40 " pdb=" C PHE H 40 " ideal model delta sigma weight residual 109.81 118.40 -8.59 2.21e+00 2.05e-01 1.51e+01 angle pdb=" N PHE E 40 " pdb=" CA PHE E 40 " pdb=" C PHE E 40 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 ... (remaining 7595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.57: 2512 11.57 - 23.15: 440 23.15 - 34.72: 160 34.72 - 46.29: 128 46.29 - 57.87: 24 Dihedral angle restraints: 3264 sinusoidal: 1232 harmonic: 2032 Sorted by residual: dihedral pdb=" CA THR A 70 " pdb=" C THR A 70 " pdb=" N SER A 71 " pdb=" CA SER A 71 " ideal model delta harmonic sigma weight residual 180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA THR E 70 " pdb=" C THR E 70 " pdb=" N SER E 71 " pdb=" CA SER E 71 " ideal model delta harmonic sigma weight residual 180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA THR G 70 " pdb=" C THR G 70 " pdb=" N SER G 71 " pdb=" CA SER G 71 " ideal model delta harmonic sigma weight residual 180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 324 0.026 - 0.051: 195 0.051 - 0.077: 125 0.077 - 0.103: 81 0.103 - 0.128: 67 Chirality restraints: 792 Sorted by residual: chirality pdb=" CG LEU C 96 " pdb=" CB LEU C 96 " pdb=" CD1 LEU C 96 " pdb=" CD2 LEU C 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL G 100 " pdb=" N VAL G 100 " pdb=" C VAL G 100 " pdb=" CB VAL G 100 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CG LEU F 96 " pdb=" CB LEU F 96 " pdb=" CD1 LEU F 96 " pdb=" CD2 LEU F 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 789 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 99 " 0.022 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP F 99 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 99 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 99 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 99 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 99 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 99 " 0.022 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" CG TRP H 99 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP H 99 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP H 99 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 99 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 99 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.022 2.00e-02 2.50e+03 1.58e-02 6.25e+00 pdb=" CG TRP B 99 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.003 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1655 2.80 - 3.33: 4706 3.33 - 3.85: 9392 3.85 - 4.38: 10364 4.38 - 4.90: 21885 Nonbonded interactions: 48002 Sorted by model distance: nonbonded pdb=" O ASN G 52 " pdb=" ND2 ASN H 52 " model vdw 2.277 3.120 nonbonded pdb=" O THR H 70 " pdb=" OG1 THR H 70 " model vdw 2.306 3.040 nonbonded pdb=" O THR B 70 " pdb=" OG1 THR B 70 " model vdw 2.306 3.040 nonbonded pdb=" O THR F 70 " pdb=" OG1 THR F 70 " model vdw 2.307 3.040 nonbonded pdb=" O THR E 70 " pdb=" OG1 THR E 70 " model vdw 2.307 3.040 ... (remaining 47997 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.780 Find NCS groups from input model: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.010 0.043 5600 Z= 0.660 Angle : 1.262 8.957 7600 Z= 0.668 Chirality : 0.056 0.128 792 Planarity : 0.009 0.051 1000 Dihedral : 16.173 57.866 1960 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.85 % Favored : 83.15 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.19), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP F 99 PHE 0.020 0.005 PHE E 63 TYR 0.013 0.003 TYR D 50 ARG 0.001 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8805 (mttt) cc_final: 0.8293 (mtpt) REVERT: A 36 TRP cc_start: 0.8826 (t-100) cc_final: 0.8563 (t-100) REVERT: A 80 GLN cc_start: 0.8796 (tt0) cc_final: 0.8535 (tt0) REVERT: B 35 LYS cc_start: 0.8338 (mttt) cc_final: 0.7694 (ttmm) REVERT: B 36 TRP cc_start: 0.8876 (t-100) cc_final: 0.8423 (t-100) REVERT: B 37 TYR cc_start: 0.8376 (t80) cc_final: 0.7268 (t80) REVERT: B 50 TYR cc_start: 0.8478 (t80) cc_final: 0.8157 (t80) REVERT: B 80 GLN cc_start: 0.8619 (tt0) cc_final: 0.8009 (tt0) REVERT: C 40 PHE cc_start: 0.8537 (m-80) cc_final: 0.8273 (m-10) REVERT: C 46 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8809 (ptpt) REVERT: D 53 ASP cc_start: 0.8613 (p0) cc_final: 0.7869 (p0) REVERT: D 80 GLN cc_start: 0.8757 (tt0) cc_final: 0.8274 (tt0) REVERT: D 82 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 87 TYR cc_start: 0.8378 (t80) cc_final: 0.8068 (t80) REVERT: E 36 TRP cc_start: 0.8881 (t-100) cc_final: 0.8388 (t-100) REVERT: E 46 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8613 (ptpp) REVERT: E 80 GLN cc_start: 0.8605 (tt0) cc_final: 0.7975 (tt0) REVERT: E 87 TYR cc_start: 0.8327 (t80) cc_final: 0.8095 (t80) REVERT: F 36 TRP cc_start: 0.8781 (t-100) cc_final: 0.8530 (t-100) REVERT: F 50 TYR cc_start: 0.8498 (t80) cc_final: 0.8186 (t80) REVERT: G 40 PHE cc_start: 0.8521 (m-80) cc_final: 0.8290 (m-10) REVERT: G 46 LYS cc_start: 0.8945 (ptpt) cc_final: 0.8676 (ptpp) REVERT: G 80 GLN cc_start: 0.8735 (tt0) cc_final: 0.8205 (tm-30) REVERT: G 82 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7842 (mt-10) REVERT: G 84 GLU cc_start: 0.8245 (mp0) cc_final: 0.8018 (mp0) REVERT: G 87 TYR cc_start: 0.8457 (t80) cc_final: 0.8169 (t80) REVERT: H 46 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8781 (ptpt) outliers start: 8 outliers final: 3 residues processed: 235 average time/residue: 0.2194 time to fit residues: 62.5000 Evaluate side-chains 190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.087783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077001 restraints weight = 15049.241| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.05 r_work: 0.3733 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5600 Z= 0.297 Angle : 0.820 8.247 7600 Z= 0.394 Chirality : 0.044 0.139 792 Planarity : 0.008 0.059 1000 Dihedral : 6.489 29.264 795 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 3.47 % Allowed : 20.14 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.27 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 PHE 0.011 0.003 PHE D 101 TYR 0.019 0.002 TYR A 88 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 35 LYS cc_start: 0.8728 (mttt) cc_final: 0.8179 (mtpt) REVERT: A 36 TRP cc_start: 0.8910 (t-100) cc_final: 0.8271 (t-100) REVERT: A 53 ASP cc_start: 0.8871 (p0) cc_final: 0.8061 (p0) REVERT: B 36 TRP cc_start: 0.8862 (t-100) cc_final: 0.8044 (t-100) REVERT: B 53 ASP cc_start: 0.8700 (p0) cc_final: 0.7501 (p0) REVERT: B 80 GLN cc_start: 0.8896 (tt0) cc_final: 0.8418 (tt0) REVERT: B 84 GLU cc_start: 0.8108 (mp0) cc_final: 0.7901 (mp0) REVERT: C 17 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8055 (mtp180) REVERT: C 40 PHE cc_start: 0.8623 (m-80) cc_final: 0.8329 (m-10) REVERT: C 67 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8194 (mttt) REVERT: C 83 ASP cc_start: 0.8169 (t0) cc_final: 0.7784 (t0) REVERT: C 101 PHE cc_start: 0.6825 (m-80) cc_final: 0.6299 (m-80) REVERT: D 40 PHE cc_start: 0.8586 (m-10) cc_final: 0.8363 (m-10) REVERT: D 53 ASP cc_start: 0.8780 (p0) cc_final: 0.7567 (p0) REVERT: D 80 GLN cc_start: 0.8895 (tt0) cc_final: 0.8653 (tt0) REVERT: D 87 TYR cc_start: 0.8471 (t80) cc_final: 0.8031 (t80) REVERT: E 36 TRP cc_start: 0.8868 (t-100) cc_final: 0.8108 (t-100) REVERT: E 46 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7996 (ptpp) REVERT: E 82 GLU cc_start: 0.8476 (mp0) cc_final: 0.8124 (mp0) REVERT: E 87 TYR cc_start: 0.8461 (t80) cc_final: 0.8123 (t80) REVERT: F 82 GLU cc_start: 0.8662 (mt-10) cc_final: 0.7950 (mp0) REVERT: F 86 ASP cc_start: 0.8441 (m-30) cc_final: 0.8130 (m-30) REVERT: G 36 TRP cc_start: 0.8661 (t-100) cc_final: 0.8296 (t-100) REVERT: G 46 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7892 (ptpp) REVERT: G 53 ASP cc_start: 0.8774 (p0) cc_final: 0.7595 (p0) REVERT: G 63 PHE cc_start: 0.8660 (t80) cc_final: 0.8048 (t80) REVERT: G 80 GLN cc_start: 0.8777 (tt0) cc_final: 0.8365 (tm-30) REVERT: G 82 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8158 (mt-10) REVERT: G 84 GLU cc_start: 0.7745 (mp0) cc_final: 0.7341 (mp0) REVERT: G 86 ASP cc_start: 0.8347 (m-30) cc_final: 0.8139 (m-30) REVERT: G 87 TYR cc_start: 0.8487 (t80) cc_final: 0.8193 (t80) REVERT: H 37 TYR cc_start: 0.7876 (t80) cc_final: 0.7450 (t80) REVERT: H 40 PHE cc_start: 0.8575 (m-10) cc_final: 0.8209 (m-10) REVERT: H 46 LYS cc_start: 0.8389 (ptpt) cc_final: 0.7831 (ptpt) REVERT: H 53 ASP cc_start: 0.8802 (p0) cc_final: 0.7816 (p0) REVERT: H 83 ASP cc_start: 0.7477 (t0) cc_final: 0.7240 (t0) outliers start: 20 outliers final: 5 residues processed: 207 average time/residue: 0.1428 time to fit residues: 39.6060 Evaluate side-chains 187 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.082961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.073082 restraints weight = 15598.888| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.92 r_work: 0.3700 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5600 Z= 0.310 Angle : 0.801 7.020 7600 Z= 0.388 Chirality : 0.043 0.138 792 Planarity : 0.007 0.050 1000 Dihedral : 6.009 23.430 792 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 1.74 % Allowed : 22.40 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 PHE 0.012 0.002 PHE G 40 TYR 0.026 0.002 TYR B 87 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.593 Fit side-chains REVERT: A 35 LYS cc_start: 0.8649 (mttt) cc_final: 0.8099 (mtpt) REVERT: A 36 TRP cc_start: 0.8837 (t-100) cc_final: 0.8374 (t-100) REVERT: A 53 ASP cc_start: 0.8829 (p0) cc_final: 0.8403 (p0) REVERT: A 88 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: B 50 TYR cc_start: 0.8055 (t80) cc_final: 0.7759 (t80) REVERT: C 17 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7991 (mtp180) REVERT: C 40 PHE cc_start: 0.8569 (m-80) cc_final: 0.8241 (m-10) REVERT: C 53 ASP cc_start: 0.8798 (p0) cc_final: 0.8586 (p0) REVERT: C 67 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8263 (mttt) REVERT: C 82 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8014 (mp0) REVERT: C 84 GLU cc_start: 0.8166 (mp0) cc_final: 0.7723 (mp0) REVERT: C 87 TYR cc_start: 0.8492 (t80) cc_final: 0.7827 (t80) REVERT: C 101 PHE cc_start: 0.6756 (m-80) cc_final: 0.6547 (m-80) REVERT: D 53 ASP cc_start: 0.8695 (p0) cc_final: 0.7523 (p0) REVERT: D 80 GLN cc_start: 0.8832 (tt0) cc_final: 0.8408 (tt0) REVERT: D 82 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7819 (mp0) REVERT: D 84 GLU cc_start: 0.8007 (mp0) cc_final: 0.7708 (mp0) REVERT: E 36 TRP cc_start: 0.8854 (t-100) cc_final: 0.8007 (t-100) REVERT: E 46 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7748 (ptpp) REVERT: E 82 GLU cc_start: 0.8447 (mp0) cc_final: 0.8094 (mp0) REVERT: E 84 GLU cc_start: 0.7909 (mp0) cc_final: 0.7683 (mp0) REVERT: E 87 TYR cc_start: 0.8361 (t80) cc_final: 0.8042 (t80) REVERT: F 17 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7757 (mtp180) REVERT: F 82 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8071 (mp0) REVERT: G 36 TRP cc_start: 0.8674 (t-100) cc_final: 0.8113 (t-100) REVERT: G 40 PHE cc_start: 0.8357 (m-10) cc_final: 0.8127 (m-10) REVERT: G 46 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7867 (ptpp) REVERT: G 53 ASP cc_start: 0.8697 (p0) cc_final: 0.7476 (p0) REVERT: G 82 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8284 (mt-10) REVERT: G 84 GLU cc_start: 0.7761 (mp0) cc_final: 0.7372 (mp0) REVERT: G 86 ASP cc_start: 0.8083 (m-30) cc_final: 0.7877 (m-30) REVERT: H 40 PHE cc_start: 0.8555 (m-10) cc_final: 0.8223 (m-10) REVERT: H 46 LYS cc_start: 0.7994 (ptpt) cc_final: 0.7657 (ptmt) REVERT: H 53 ASP cc_start: 0.8762 (p0) cc_final: 0.7802 (p0) outliers start: 10 outliers final: 5 residues processed: 197 average time/residue: 0.1515 time to fit residues: 39.2702 Evaluate side-chains 192 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.081747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.071901 restraints weight = 16953.155| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.03 r_work: 0.3558 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 5600 Z= 0.528 Angle : 0.937 7.637 7600 Z= 0.468 Chirality : 0.045 0.134 792 Planarity : 0.007 0.046 1000 Dihedral : 6.719 26.260 792 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.82 % Favored : 81.18 % Rotamer: Outliers : 2.43 % Allowed : 24.83 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP H 99 PHE 0.015 0.003 PHE G 40 TYR 0.024 0.003 TYR B 87 ARG 0.003 0.001 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.572 Fit side-chains REVERT: A 35 LYS cc_start: 0.8739 (mttt) cc_final: 0.8148 (mtpt) REVERT: A 36 TRP cc_start: 0.8967 (t-100) cc_final: 0.8568 (t-100) REVERT: A 53 ASP cc_start: 0.8759 (p0) cc_final: 0.8342 (p0) REVERT: A 88 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: B 50 TYR cc_start: 0.8052 (t80) cc_final: 0.7711 (t80) REVERT: B 80 GLN cc_start: 0.9053 (tt0) cc_final: 0.8730 (mt0) REVERT: C 40 PHE cc_start: 0.8650 (m-80) cc_final: 0.8410 (m-10) REVERT: C 67 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8396 (mttt) REVERT: C 84 GLU cc_start: 0.8375 (mp0) cc_final: 0.7867 (mp0) REVERT: D 53 ASP cc_start: 0.8776 (p0) cc_final: 0.7473 (p0) REVERT: D 80 GLN cc_start: 0.8933 (tt0) cc_final: 0.8634 (tt0) REVERT: D 82 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8070 (mp0) REVERT: D 84 GLU cc_start: 0.8179 (mp0) cc_final: 0.7630 (mp0) REVERT: E 36 TRP cc_start: 0.8971 (t-100) cc_final: 0.8247 (t-100) REVERT: E 46 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7879 (ptpp) REVERT: E 53 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.7929 (p0) REVERT: E 82 GLU cc_start: 0.8457 (mp0) cc_final: 0.8067 (mp0) REVERT: E 83 ASP cc_start: 0.8051 (t0) cc_final: 0.7850 (t0) REVERT: E 86 ASP cc_start: 0.8454 (m-30) cc_final: 0.8177 (m-30) REVERT: F 82 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8180 (mp0) REVERT: F 88 TYR cc_start: 0.8905 (m-80) cc_final: 0.8535 (m-80) REVERT: G 46 LYS cc_start: 0.8181 (ptpt) cc_final: 0.7892 (ptpp) REVERT: G 53 ASP cc_start: 0.8708 (p0) cc_final: 0.7515 (p0) REVERT: G 82 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8427 (mt-10) REVERT: G 84 GLU cc_start: 0.7917 (mp0) cc_final: 0.7661 (mp0) REVERT: G 86 ASP cc_start: 0.8215 (m-30) cc_final: 0.7966 (m-30) REVERT: H 40 PHE cc_start: 0.8511 (m-10) cc_final: 0.8259 (m-10) REVERT: H 46 LYS cc_start: 0.7870 (ptpt) cc_final: 0.7343 (ptpt) REVERT: H 50 TYR cc_start: 0.8810 (t80) cc_final: 0.8585 (t80) outliers start: 14 outliers final: 6 residues processed: 184 average time/residue: 0.1257 time to fit residues: 31.6729 Evaluate side-chains 180 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.083660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.073940 restraints weight = 15973.010| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.95 r_work: 0.3658 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5600 Z= 0.282 Angle : 0.794 7.438 7600 Z= 0.383 Chirality : 0.044 0.136 792 Planarity : 0.006 0.046 1000 Dihedral : 6.009 25.072 792 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 2.08 % Allowed : 25.00 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 92 PHE 0.014 0.002 PHE G 40 TYR 0.020 0.001 TYR B 87 ARG 0.002 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.613 Fit side-chains REVERT: A 35 LYS cc_start: 0.8743 (mttt) cc_final: 0.8141 (mtpt) REVERT: A 36 TRP cc_start: 0.8861 (t-100) cc_final: 0.8484 (t-100) REVERT: A 53 ASP cc_start: 0.8799 (p0) cc_final: 0.8106 (p0) REVERT: A 88 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: B 50 TYR cc_start: 0.8101 (t80) cc_final: 0.7759 (t80) REVERT: B 63 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7907 (t80) REVERT: C 40 PHE cc_start: 0.8607 (m-80) cc_final: 0.8316 (m-10) REVERT: C 67 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8320 (mttt) REVERT: C 82 GLU cc_start: 0.8742 (mt-10) cc_final: 0.7943 (mp0) REVERT: C 84 GLU cc_start: 0.8385 (mp0) cc_final: 0.7716 (mp0) REVERT: D 53 ASP cc_start: 0.8763 (p0) cc_final: 0.7447 (p0) REVERT: D 63 PHE cc_start: 0.8616 (t80) cc_final: 0.7508 (t80) REVERT: D 80 GLN cc_start: 0.8857 (tt0) cc_final: 0.8401 (tt0) REVERT: D 82 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7911 (mp0) REVERT: D 84 GLU cc_start: 0.8165 (mp0) cc_final: 0.7653 (mp0) REVERT: E 36 TRP cc_start: 0.8881 (t-100) cc_final: 0.8038 (t-100) REVERT: E 46 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7659 (ptpp) REVERT: E 53 ASP cc_start: 0.8762 (p0) cc_final: 0.7466 (p0) REVERT: E 63 PHE cc_start: 0.8555 (t80) cc_final: 0.7623 (t80) REVERT: E 82 GLU cc_start: 0.8362 (mp0) cc_final: 0.7970 (mp0) REVERT: E 86 ASP cc_start: 0.8385 (m-30) cc_final: 0.8044 (m-30) REVERT: F 17 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7763 (mtp180) REVERT: F 63 PHE cc_start: 0.8671 (t80) cc_final: 0.7876 (t80) REVERT: F 82 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8164 (mp0) REVERT: G 36 TRP cc_start: 0.8712 (t-100) cc_final: 0.8124 (t-100) REVERT: G 40 PHE cc_start: 0.8431 (m-10) cc_final: 0.8068 (m-10) REVERT: G 46 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7960 (ptpp) REVERT: G 53 ASP cc_start: 0.8602 (p0) cc_final: 0.7392 (p0) REVERT: G 82 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8423 (mt-10) REVERT: G 84 GLU cc_start: 0.8088 (mp0) cc_final: 0.7692 (mp0) REVERT: H 39 GLN cc_start: 0.7824 (tt0) cc_final: 0.7349 (mt0) REVERT: H 40 PHE cc_start: 0.8639 (m-10) cc_final: 0.8371 (m-80) REVERT: H 46 LYS cc_start: 0.7940 (ptpt) cc_final: 0.7360 (ptpt) REVERT: H 53 ASP cc_start: 0.8695 (p0) cc_final: 0.8385 (p0) outliers start: 12 outliers final: 7 residues processed: 186 average time/residue: 0.1404 time to fit residues: 34.9150 Evaluate side-chains 188 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.081601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.071615 restraints weight = 15647.895| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.97 r_work: 0.3650 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5600 Z= 0.299 Angle : 0.801 7.623 7600 Z= 0.385 Chirality : 0.043 0.134 792 Planarity : 0.006 0.043 1000 Dihedral : 5.809 25.695 792 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.03 % Favored : 84.97 % Rotamer: Outliers : 2.95 % Allowed : 25.87 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 92 PHE 0.013 0.002 PHE E 40 TYR 0.020 0.001 TYR B 87 ARG 0.002 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.654 Fit side-chains REVERT: A 36 TRP cc_start: 0.8924 (t-100) cc_final: 0.8530 (t-100) REVERT: A 55 ARG cc_start: 0.8447 (ttm110) cc_final: 0.7870 (mtt90) REVERT: A 88 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: B 50 TYR cc_start: 0.8127 (t80) cc_final: 0.7748 (t80) REVERT: B 63 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8068 (t80) REVERT: C 40 PHE cc_start: 0.8613 (m-80) cc_final: 0.8386 (m-10) REVERT: C 67 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8367 (mttt) REVERT: C 82 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8007 (mp0) REVERT: C 84 GLU cc_start: 0.8424 (mp0) cc_final: 0.7758 (mp0) REVERT: D 53 ASP cc_start: 0.8773 (p0) cc_final: 0.7422 (p0) REVERT: D 63 PHE cc_start: 0.8705 (t80) cc_final: 0.7639 (t80) REVERT: D 80 GLN cc_start: 0.8873 (tt0) cc_final: 0.8387 (tt0) REVERT: D 82 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8055 (mp0) REVERT: D 84 GLU cc_start: 0.8084 (mp0) cc_final: 0.7658 (mp0) REVERT: E 46 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7746 (ptpp) REVERT: E 53 ASP cc_start: 0.8842 (p0) cc_final: 0.7504 (p0) REVERT: E 63 PHE cc_start: 0.8630 (t80) cc_final: 0.7441 (t80) REVERT: E 82 GLU cc_start: 0.8393 (mp0) cc_final: 0.8139 (mp0) REVERT: E 86 ASP cc_start: 0.8491 (m-30) cc_final: 0.8168 (m-30) REVERT: F 17 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7821 (mtp180) REVERT: F 63 PHE cc_start: 0.8751 (t80) cc_final: 0.7830 (t80) REVERT: F 82 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8171 (mp0) REVERT: G 36 TRP cc_start: 0.8794 (t-100) cc_final: 0.8190 (t-100) REVERT: G 40 PHE cc_start: 0.8302 (m-10) cc_final: 0.7952 (m-10) REVERT: G 46 LYS cc_start: 0.8261 (ptpt) cc_final: 0.8004 (ptpp) REVERT: G 53 ASP cc_start: 0.8749 (p0) cc_final: 0.7440 (p0) REVERT: G 82 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8460 (mt-10) REVERT: G 84 GLU cc_start: 0.8064 (mp0) cc_final: 0.7560 (mp0) REVERT: H 39 GLN cc_start: 0.7914 (tt0) cc_final: 0.7395 (mt0) REVERT: H 40 PHE cc_start: 0.8667 (m-10) cc_final: 0.8341 (m-10) REVERT: H 46 LYS cc_start: 0.8027 (ptpt) cc_final: 0.7463 (ptpt) REVERT: H 53 ASP cc_start: 0.8795 (p0) cc_final: 0.8494 (p0) outliers start: 17 outliers final: 9 residues processed: 189 average time/residue: 0.1503 time to fit residues: 37.5311 Evaluate side-chains 190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.082252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.072204 restraints weight = 15616.431| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.96 r_work: 0.3652 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5600 Z= 0.309 Angle : 0.807 8.111 7600 Z= 0.385 Chirality : 0.044 0.138 792 Planarity : 0.006 0.044 1000 Dihedral : 5.795 26.049 792 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 2.78 % Allowed : 26.39 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 36 PHE 0.029 0.002 PHE D 40 TYR 0.018 0.001 TYR B 87 ARG 0.003 0.000 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8890 (t-100) cc_final: 0.8509 (t-100) REVERT: A 55 ARG cc_start: 0.8437 (ttm110) cc_final: 0.7901 (mtt90) REVERT: A 88 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: B 50 TYR cc_start: 0.8085 (t80) cc_final: 0.7742 (t80) REVERT: B 63 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8083 (t80) REVERT: C 40 PHE cc_start: 0.8564 (m-80) cc_final: 0.8358 (m-10) REVERT: C 67 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8338 (mttt) REVERT: C 82 GLU cc_start: 0.8792 (mt-10) cc_final: 0.7993 (mp0) REVERT: C 84 GLU cc_start: 0.8437 (mp0) cc_final: 0.7745 (mp0) REVERT: C 87 TYR cc_start: 0.8359 (t80) cc_final: 0.7736 (t80) REVERT: D 53 ASP cc_start: 0.8715 (p0) cc_final: 0.7363 (p0) REVERT: D 63 PHE cc_start: 0.8658 (t80) cc_final: 0.7544 (t80) REVERT: D 80 GLN cc_start: 0.8879 (tt0) cc_final: 0.8379 (tt0) REVERT: D 82 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8018 (mp0) REVERT: D 84 GLU cc_start: 0.8131 (mp0) cc_final: 0.7635 (mp0) REVERT: E 36 TRP cc_start: 0.9066 (t-100) cc_final: 0.8378 (t-100) REVERT: E 46 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7677 (ptpp) REVERT: E 53 ASP cc_start: 0.8840 (p0) cc_final: 0.7495 (p0) REVERT: E 63 PHE cc_start: 0.8605 (t80) cc_final: 0.7359 (t80) REVERT: E 82 GLU cc_start: 0.8501 (mp0) cc_final: 0.8235 (mp0) REVERT: E 86 ASP cc_start: 0.8513 (m-30) cc_final: 0.8178 (m-30) REVERT: F 17 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7797 (mtp180) REVERT: F 63 PHE cc_start: 0.8726 (t80) cc_final: 0.7795 (t80) REVERT: F 82 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8164 (mp0) REVERT: F 84 GLU cc_start: 0.8025 (mp0) cc_final: 0.7792 (mp0) REVERT: G 36 TRP cc_start: 0.8758 (t-100) cc_final: 0.8150 (t-100) REVERT: G 40 PHE cc_start: 0.8223 (m-10) cc_final: 0.7728 (m-80) REVERT: G 46 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7937 (ptpp) REVERT: G 53 ASP cc_start: 0.8723 (p0) cc_final: 0.7438 (p0) REVERT: G 82 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8407 (mt-10) REVERT: G 84 GLU cc_start: 0.7994 (mp0) cc_final: 0.7538 (mp0) REVERT: H 39 GLN cc_start: 0.7880 (tt0) cc_final: 0.7548 (mt0) REVERT: H 40 PHE cc_start: 0.8678 (m-10) cc_final: 0.8471 (m-80) REVERT: H 46 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7419 (ptpt) REVERT: H 53 ASP cc_start: 0.8786 (p0) cc_final: 0.8472 (p0) REVERT: H 83 ASP cc_start: 0.7629 (t0) cc_final: 0.7414 (t0) outliers start: 16 outliers final: 11 residues processed: 187 average time/residue: 0.1375 time to fit residues: 34.5824 Evaluate side-chains 190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.085986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.076588 restraints weight = 15574.572| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.79 r_work: 0.3743 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5600 Z= 0.244 Angle : 0.772 8.486 7600 Z= 0.360 Chirality : 0.044 0.136 792 Planarity : 0.005 0.040 1000 Dihedral : 5.394 25.858 792 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 2.78 % Allowed : 26.04 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 92 PHE 0.024 0.002 PHE D 40 TYR 0.018 0.001 TYR B 87 ARG 0.003 0.000 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8912 (t-100) cc_final: 0.8503 (t-100) REVERT: A 55 ARG cc_start: 0.8450 (ttm110) cc_final: 0.7810 (mtt90) REVERT: A 88 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: B 50 TYR cc_start: 0.8075 (t80) cc_final: 0.7753 (t80) REVERT: B 63 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8041 (t80) REVERT: C 17 ARG cc_start: 0.8313 (mtt180) cc_final: 0.8071 (mtp180) REVERT: C 40 PHE cc_start: 0.8613 (m-80) cc_final: 0.8379 (m-10) REVERT: C 53 ASP cc_start: 0.8599 (p0) cc_final: 0.7574 (p0) REVERT: C 67 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8289 (mttt) REVERT: C 82 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8103 (mp0) REVERT: C 84 GLU cc_start: 0.8404 (mp0) cc_final: 0.7690 (mp0) REVERT: D 29 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8243 (tp) REVERT: D 53 ASP cc_start: 0.8687 (p0) cc_final: 0.7261 (p0) REVERT: D 63 PHE cc_start: 0.8674 (t80) cc_final: 0.7680 (t80) REVERT: D 80 GLN cc_start: 0.8879 (tt0) cc_final: 0.8204 (tt0) REVERT: D 82 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7970 (mp0) REVERT: D 84 GLU cc_start: 0.8016 (mp0) cc_final: 0.7496 (mp0) REVERT: E 46 LYS cc_start: 0.7971 (ptpt) cc_final: 0.7748 (ptpp) REVERT: E 53 ASP cc_start: 0.8830 (p0) cc_final: 0.7605 (p0) REVERT: E 63 PHE cc_start: 0.8619 (t80) cc_final: 0.7407 (t80) REVERT: E 82 GLU cc_start: 0.8508 (mp0) cc_final: 0.8173 (mp0) REVERT: E 86 ASP cc_start: 0.8503 (m-30) cc_final: 0.8231 (m-30) REVERT: F 17 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7794 (mtp180) REVERT: F 63 PHE cc_start: 0.8681 (t80) cc_final: 0.7674 (t80) REVERT: F 82 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8082 (mp0) REVERT: G 36 TRP cc_start: 0.8786 (t-100) cc_final: 0.8155 (t-100) REVERT: G 40 PHE cc_start: 0.8201 (m-10) cc_final: 0.7647 (m-80) REVERT: G 46 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7942 (ptpp) REVERT: G 53 ASP cc_start: 0.8700 (p0) cc_final: 0.7410 (p0) REVERT: G 71 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7558 (m) REVERT: G 82 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8096 (mp0) REVERT: G 84 GLU cc_start: 0.8105 (mp0) cc_final: 0.7610 (mp0) REVERT: G 87 TYR cc_start: 0.8288 (t80) cc_final: 0.8005 (t80) REVERT: H 39 GLN cc_start: 0.8087 (tt0) cc_final: 0.7781 (mt0) REVERT: H 46 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7571 (ptpt) REVERT: H 53 ASP cc_start: 0.8778 (p0) cc_final: 0.7757 (p0) REVERT: H 83 ASP cc_start: 0.7999 (t0) cc_final: 0.7767 (t0) outliers start: 16 outliers final: 9 residues processed: 193 average time/residue: 0.1504 time to fit residues: 38.7414 Evaluate side-chains 192 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.082566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.073605 restraints weight = 16210.959| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.75 r_work: 0.3636 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5600 Z= 0.405 Angle : 0.861 7.588 7600 Z= 0.418 Chirality : 0.045 0.141 792 Planarity : 0.005 0.044 1000 Dihedral : 5.955 27.477 792 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.42 % Favored : 82.58 % Rotamer: Outliers : 2.95 % Allowed : 27.26 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 36 PHE 0.030 0.003 PHE D 40 TYR 0.018 0.002 TYR B 87 ARG 0.003 0.000 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8972 (t-100) cc_final: 0.8586 (t-100) REVERT: A 55 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7806 (mtt90) REVERT: A 88 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: B 50 TYR cc_start: 0.8118 (t80) cc_final: 0.7696 (t80) REVERT: B 82 GLU cc_start: 0.8406 (mp0) cc_final: 0.8101 (mp0) REVERT: C 40 PHE cc_start: 0.8649 (m-80) cc_final: 0.8438 (m-10) REVERT: C 67 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8312 (mttt) REVERT: C 82 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8133 (mp0) REVERT: C 84 GLU cc_start: 0.8469 (mp0) cc_final: 0.7837 (mp0) REVERT: C 87 TYR cc_start: 0.8484 (t80) cc_final: 0.7860 (t80) REVERT: D 53 ASP cc_start: 0.8694 (p0) cc_final: 0.7254 (p0) REVERT: D 63 PHE cc_start: 0.8739 (t80) cc_final: 0.7570 (t80) REVERT: D 82 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7943 (mp0) REVERT: D 84 GLU cc_start: 0.8169 (mp0) cc_final: 0.7652 (mp0) REVERT: E 46 LYS cc_start: 0.7999 (ptpt) cc_final: 0.7729 (ptpp) REVERT: E 53 ASP cc_start: 0.8836 (p0) cc_final: 0.7456 (p0) REVERT: E 63 PHE cc_start: 0.8655 (t80) cc_final: 0.7650 (t80) REVERT: E 82 GLU cc_start: 0.8568 (mp0) cc_final: 0.8324 (mp0) REVERT: E 86 ASP cc_start: 0.8654 (m-30) cc_final: 0.8304 (m-30) REVERT: F 17 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7836 (mtp180) REVERT: F 63 PHE cc_start: 0.8844 (t80) cc_final: 0.8026 (t80) REVERT: F 82 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8195 (mp0) REVERT: F 84 GLU cc_start: 0.8209 (mp0) cc_final: 0.7988 (mp0) REVERT: G 40 PHE cc_start: 0.8466 (m-10) cc_final: 0.8029 (m-10) REVERT: G 46 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7947 (ptpp) REVERT: G 53 ASP cc_start: 0.8763 (p0) cc_final: 0.7453 (p0) REVERT: G 71 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7620 (m) REVERT: G 82 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8429 (mt-10) REVERT: G 84 GLU cc_start: 0.8188 (mp0) cc_final: 0.7718 (mp0) REVERT: H 37 TYR cc_start: 0.7547 (t80) cc_final: 0.6721 (t80) REVERT: H 40 PHE cc_start: 0.8503 (m-80) cc_final: 0.8080 (m-80) REVERT: H 46 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7459 (ptpt) REVERT: H 53 ASP cc_start: 0.8758 (p0) cc_final: 0.8437 (p0) outliers start: 17 outliers final: 12 residues processed: 190 average time/residue: 0.1577 time to fit residues: 39.6554 Evaluate side-chains 195 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.081249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.071180 restraints weight = 15980.022| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.96 r_work: 0.3698 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5600 Z= 0.277 Angle : 0.810 8.122 7600 Z= 0.386 Chirality : 0.045 0.135 792 Planarity : 0.005 0.041 1000 Dihedral : 5.652 26.855 792 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 2.43 % Allowed : 27.60 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 36 PHE 0.029 0.002 PHE D 40 TYR 0.017 0.001 TYR B 87 ARG 0.003 0.000 ARG D 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 36 TRP cc_start: 0.9024 (t-100) cc_final: 0.8636 (t-100) REVERT: A 55 ARG cc_start: 0.8509 (ttm110) cc_final: 0.7907 (mtt90) REVERT: A 63 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7655 (t80) REVERT: A 88 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: B 50 TYR cc_start: 0.8200 (t80) cc_final: 0.7828 (t80) REVERT: B 63 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 40 PHE cc_start: 0.8658 (m-80) cc_final: 0.8405 (m-10) REVERT: C 67 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8330 (mttt) REVERT: C 82 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8220 (mp0) REVERT: C 84 GLU cc_start: 0.8536 (mp0) cc_final: 0.7895 (mp0) REVERT: D 53 ASP cc_start: 0.8747 (p0) cc_final: 0.7344 (p0) REVERT: D 63 PHE cc_start: 0.8743 (t80) cc_final: 0.7749 (t80) REVERT: D 80 GLN cc_start: 0.8879 (tt0) cc_final: 0.8457 (tt0) REVERT: D 82 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8104 (mp0) REVERT: D 84 GLU cc_start: 0.8126 (mp0) cc_final: 0.7682 (mp0) REVERT: E 36 TRP cc_start: 0.8785 (t-100) cc_final: 0.8566 (t-100) REVERT: E 46 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7879 (ptpp) REVERT: E 53 ASP cc_start: 0.8935 (p0) cc_final: 0.7676 (p0) REVERT: E 63 PHE cc_start: 0.8652 (t80) cc_final: 0.7549 (t80) REVERT: E 82 GLU cc_start: 0.8572 (mp0) cc_final: 0.8230 (mp0) REVERT: E 86 ASP cc_start: 0.8710 (m-30) cc_final: 0.8317 (m-30) REVERT: F 17 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7895 (mtp180) REVERT: F 63 PHE cc_start: 0.8799 (t80) cc_final: 0.7914 (t80) REVERT: F 82 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8158 (mp0) REVERT: F 84 GLU cc_start: 0.8224 (mp0) cc_final: 0.8009 (mp0) REVERT: G 36 TRP cc_start: 0.8783 (t-100) cc_final: 0.8225 (t-100) REVERT: G 46 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8141 (ptpp) REVERT: G 53 ASP cc_start: 0.8836 (p0) cc_final: 0.7567 (p0) REVERT: G 71 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7698 (m) REVERT: G 82 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8191 (mp0) REVERT: G 84 GLU cc_start: 0.8224 (mp0) cc_final: 0.7715 (mp0) REVERT: G 87 TYR cc_start: 0.8415 (t80) cc_final: 0.8158 (t80) REVERT: H 40 PHE cc_start: 0.8619 (m-80) cc_final: 0.8237 (m-10) REVERT: H 46 LYS cc_start: 0.8296 (ptpt) cc_final: 0.7724 (ptpt) REVERT: H 53 ASP cc_start: 0.8895 (p0) cc_final: 0.8609 (p0) outliers start: 14 outliers final: 10 residues processed: 188 average time/residue: 0.1434 time to fit residues: 36.1774 Evaluate side-chains 193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.083902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.073996 restraints weight = 15722.845| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.92 r_work: 0.3724 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5600 Z= 0.262 Angle : 0.790 8.016 7600 Z= 0.373 Chirality : 0.045 0.133 792 Planarity : 0.005 0.040 1000 Dihedral : 5.445 26.554 792 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 2.26 % Allowed : 28.47 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 36 PHE 0.026 0.002 PHE D 40 TYR 0.017 0.001 TYR B 87 ARG 0.003 0.000 ARG D 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.36 seconds wall clock time: 47 minutes 11.74 seconds (2831.74 seconds total)