Starting phenix.real_space_refine on Mon Sep 23 21:14:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/09_2024/6ic3_4452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/09_2024/6ic3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/09_2024/6ic3_4452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/09_2024/6ic3_4452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/09_2024/6ic3_4452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/09_2024/6ic3_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.47, per 1000 atoms: 0.45 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 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: 1.24 Conformation dependent library (CDL) restraints added in 676.9 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: 0.70 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: 1.16 Time building geometry restraints manager: 1.46 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: 107 46.29 - 57.87: 24 Dihedral angle restraints: 3243 sinusoidal: 1211 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 3240 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: 2.02 - 2.59: 131 2.59 - 3.17: 4242 3.17 - 3.75: 8910 3.75 - 4.32: 11586 4.32 - 4.90: 23154 Nonbonded interactions: 48023 Sorted by model distance: nonbonded pdb=" SG CYS B 22 " pdb=" SG CYS B 89 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 89 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 89 " model vdw 2.018 3.760 ... (remaining 48018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.150 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.090 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- 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= 0.659 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 : 2.017 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 fitting. rotamer outliers: 8 poor density : 227 time to evaluate : 0.644 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: 0.2375 time to fit residues: 67.9969 Evaluate side-chains 190 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2666 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= 0.298 Angle : 0.828 8.062 7600 Z= 0.400 Chirality : 0.044 0.135 792 Planarity : 0.008 0.060 1000 Dihedral : 6.557 29.586 795 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 3.47 % Allowed : 22.57 % Favored : 73.96 % 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: -5.31 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (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 0.018 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 216 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 35 LYS cc_start: 0.8744 (mttt) cc_final: 0.8249 (mtpt) REVERT: A 36 TRP cc_start: 0.8806 (t-100) cc_final: 0.8449 (t-100) REVERT: A 53 ASP cc_start: 0.8504 (p0) cc_final: 0.7679 (p0) REVERT: B 36 TRP cc_start: 0.8678 (t-100) cc_final: 0.8250 (t-100) REVERT: B 40 PHE cc_start: 0.8462 (m-10) cc_final: 0.8229 (m-10) REVERT: B 53 ASP cc_start: 0.8641 (p0) cc_final: 0.7463 (p0) REVERT: B 80 GLN cc_start: 0.8304 (tt0) cc_final: 0.7832 (tt0) REVERT: B 87 TYR cc_start: 0.8746 (t80) cc_final: 0.8511 (t80) REVERT: C 40 PHE cc_start: 0.8416 (m-80) cc_final: 0.8106 (m-10) REVERT: C 46 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8766 (ptpt) REVERT: C 67 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8355 (mttt) REVERT: C 83 ASP cc_start: 0.8635 (t0) cc_final: 0.8423 (t0) REVERT: C 101 PHE cc_start: 0.7137 (m-80) cc_final: 0.6703 (m-80) REVERT: D 53 ASP cc_start: 0.8568 (p0) cc_final: 0.7387 (p0) REVERT: D 80 GLN cc_start: 0.8632 (tt0) cc_final: 0.8246 (tt0) REVERT: D 82 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8184 (mt-10) REVERT: D 87 TYR cc_start: 0.8606 (t80) cc_final: 0.8082 (t80) REVERT: E 36 TRP cc_start: 0.8745 (t-100) cc_final: 0.8186 (t-100) REVERT: E 46 LYS cc_start: 0.8987 (ptpt) cc_final: 0.8689 (ptpp) REVERT: E 87 TYR cc_start: 0.8563 (t80) cc_final: 0.8249 (t80) REVERT: F 82 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8011 (mp0) REVERT: G 46 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8503 (ptpp) REVERT: G 53 ASP cc_start: 0.8434 (p0) cc_final: 0.7253 (p0) REVERT: G 63 PHE cc_start: 0.8547 (t80) cc_final: 0.8304 (t80) REVERT: G 82 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8026 (mt-10) REVERT: G 84 GLU cc_start: 0.8243 (mp0) cc_final: 0.7907 (mp0) REVERT: H 37 TYR cc_start: 0.7603 (t80) cc_final: 0.7318 (t80) REVERT: H 40 PHE cc_start: 0.8511 (m-10) cc_final: 0.8238 (m-10) REVERT: H 46 LYS cc_start: 0.8957 (ptpt) cc_final: 0.8322 (ptpt) REVERT: H 53 ASP cc_start: 0.8245 (p0) cc_final: 0.7265 (p0) outliers start: 20 outliers final: 5 residues processed: 205 average time/residue: 0.1447 time to fit residues: 39.5143 Evaluate side-chains 187 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 36 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 5600 Z= 0.574 Angle : 0.975 7.461 7600 Z= 0.490 Chirality : 0.045 0.139 792 Planarity : 0.007 0.050 1000 Dihedral : 7.123 25.426 792 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.80 % Favored : 80.20 % Rotamer: Outliers : 3.82 % Allowed : 23.96 % Favored : 72.22 % 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: -5.38 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP H 99 PHE 0.016 0.003 PHE G 40 TYR 0.019 0.003 TYR D 88 ARG 0.004 0.001 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 206 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 0.563 Fit side-chains REVERT: A 35 LYS cc_start: 0.8852 (mttt) cc_final: 0.8370 (mtpt) REVERT: A 36 TRP cc_start: 0.8996 (t-100) cc_final: 0.8644 (t-100) REVERT: B 50 TYR cc_start: 0.8268 (t80) cc_final: 0.7895 (t80) REVERT: B 80 GLN cc_start: 0.8535 (tt0) cc_final: 0.8252 (mt0) REVERT: C 40 PHE cc_start: 0.8550 (m-80) cc_final: 0.8318 (m-10) REVERT: D 53 ASP cc_start: 0.8664 (p0) cc_final: 0.7367 (p0) REVERT: D 80 GLN cc_start: 0.8737 (tt0) cc_final: 0.7855 (tt0) REVERT: D 82 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8196 (mp0) REVERT: E 36 TRP cc_start: 0.8990 (t-100) cc_final: 0.8595 (t-100) REVERT: E 46 LYS cc_start: 0.8961 (ptpt) cc_final: 0.8671 (ptpp) REVERT: E 83 ASP cc_start: 0.8590 (t0) cc_final: 0.8334 (t0) REVERT: G 40 PHE cc_start: 0.8385 (m-10) cc_final: 0.8097 (m-10) REVERT: G 46 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8603 (ptpp) REVERT: G 53 ASP cc_start: 0.8611 (p0) cc_final: 0.7301 (p0) REVERT: G 80 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8061 (tm-30) REVERT: G 82 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8390 (mt-10) REVERT: G 86 ASP cc_start: 0.8334 (m-30) cc_final: 0.8110 (m-30) REVERT: H 36 TRP cc_start: 0.8954 (t-100) cc_final: 0.8624 (t-100) REVERT: H 40 PHE cc_start: 0.8553 (m-10) cc_final: 0.8286 (m-10) REVERT: H 46 LYS cc_start: 0.8795 (ptpt) cc_final: 0.8126 (ptpt) outliers start: 22 outliers final: 10 residues processed: 194 average time/residue: 0.1363 time to fit residues: 35.5199 Evaluate side-chains 182 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 74 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 80 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5600 Z= 0.253 Angle : 0.792 7.464 7600 Z= 0.385 Chirality : 0.044 0.135 792 Planarity : 0.006 0.045 1000 Dihedral : 6.061 24.170 792 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.60 % Allowed : 24.65 % 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: -5.25 (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 0.013 0.002 TRP B 92 PHE 0.013 0.002 PHE G 40 TYR 0.011 0.001 TYR G 87 ARG 0.002 0.000 ARG B 25 *********************** 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 202 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 0.637 Fit side-chains REVERT: A 35 LYS cc_start: 0.8787 (mttt) cc_final: 0.8234 (mtpt) REVERT: A 36 TRP cc_start: 0.8809 (t-100) cc_final: 0.8594 (t-100) REVERT: A 53 ASP cc_start: 0.8562 (p0) cc_final: 0.7490 (p0) REVERT: B 37 TYR cc_start: 0.8478 (t80) cc_final: 0.7372 (t80) REVERT: B 50 TYR cc_start: 0.8306 (t80) cc_final: 0.7936 (t80) REVERT: B 53 ASP cc_start: 0.8594 (p0) cc_final: 0.7350 (p0) REVERT: C 37 TYR cc_start: 0.8329 (t80) cc_final: 0.8076 (t80) REVERT: C 40 PHE cc_start: 0.8448 (m-80) cc_final: 0.8221 (m-10) REVERT: C 53 ASP cc_start: 0.8487 (p0) cc_final: 0.8261 (p0) REVERT: C 67 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8506 (mttt) REVERT: C 82 GLU cc_start: 0.8441 (mp0) cc_final: 0.7785 (mp0) REVERT: C 88 TYR cc_start: 0.8079 (m-80) cc_final: 0.7604 (t80) REVERT: D 53 ASP cc_start: 0.8608 (p0) cc_final: 0.7470 (p0) REVERT: D 80 GLN cc_start: 0.8540 (tt0) cc_final: 0.7472 (tt0) REVERT: D 82 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8152 (mp0) REVERT: E 36 TRP cc_start: 0.8763 (t-100) cc_final: 0.8235 (t-100) REVERT: E 46 LYS cc_start: 0.8884 (ptpt) cc_final: 0.8535 (ptpp) REVERT: E 82 GLU cc_start: 0.8475 (mp0) cc_final: 0.8175 (mp0) REVERT: F 63 PHE cc_start: 0.8509 (t80) cc_final: 0.8225 (t80) REVERT: G 40 PHE cc_start: 0.8188 (m-10) cc_final: 0.7807 (m-80) REVERT: G 46 LYS cc_start: 0.8904 (ptpt) cc_final: 0.8576 (ptpp) REVERT: G 53 ASP cc_start: 0.8411 (p0) cc_final: 0.7240 (p0) REVERT: G 80 GLN cc_start: 0.8530 (tm-30) cc_final: 0.7759 (tm-30) REVERT: G 82 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8297 (mt-10) REVERT: H 40 PHE cc_start: 0.8544 (m-10) cc_final: 0.8333 (m-10) REVERT: H 46 LYS cc_start: 0.8857 (ptpt) cc_final: 0.8149 (ptpt) REVERT: H 53 ASP cc_start: 0.8246 (p0) cc_final: 0.7282 (p0) outliers start: 15 outliers final: 5 residues processed: 194 average time/residue: 0.1384 time to fit residues: 35.9349 Evaluate side-chains 181 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4026 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= 0.248 Angle : 0.775 7.495 7600 Z= 0.369 Chirality : 0.043 0.141 792 Planarity : 0.006 0.044 1000 Dihedral : 5.645 23.346 792 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 2.08 % Allowed : 26.39 % Favored : 71.53 % 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 0.011 0.002 TRP E 92 PHE 0.023 0.002 PHE D 40 TYR 0.012 0.001 TYR G 87 ARG 0.002 0.000 ARG E 62 *********************** 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 195 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 0.640 Fit side-chains REVERT: A 36 TRP cc_start: 0.8824 (t-100) cc_final: 0.8483 (t-100) REVERT: A 55 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8068 (mtt90) REVERT: B 37 TYR cc_start: 0.8503 (t80) cc_final: 0.7369 (t80) REVERT: B 50 TYR cc_start: 0.8316 (t80) cc_final: 0.7983 (t80) REVERT: B 76 VAL cc_start: 0.8985 (t) cc_final: 0.8581 (p) REVERT: C 40 PHE cc_start: 0.8407 (m-80) cc_final: 0.8195 (m-10) REVERT: C 53 ASP cc_start: 0.8489 (p0) cc_final: 0.7331 (p0) REVERT: C 67 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8526 (mttt) REVERT: C 82 GLU cc_start: 0.8479 (mp0) cc_final: 0.7840 (mp0) REVERT: D 53 ASP cc_start: 0.8587 (p0) cc_final: 0.7352 (p0) REVERT: D 63 PHE cc_start: 0.8388 (t80) cc_final: 0.7960 (t80) REVERT: D 80 GLN cc_start: 0.8568 (tt0) cc_final: 0.7575 (tt0) REVERT: D 82 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8215 (mp0) REVERT: E 36 TRP cc_start: 0.8715 (t-100) cc_final: 0.8134 (t-100) REVERT: E 46 LYS cc_start: 0.8828 (ptpt) cc_final: 0.8483 (ptpp) REVERT: E 53 ASP cc_start: 0.8525 (p0) cc_final: 0.7250 (p0) REVERT: E 63 PHE cc_start: 0.8316 (t80) cc_final: 0.7784 (t80) REVERT: F 63 PHE cc_start: 0.8482 (t80) cc_final: 0.8087 (t80) REVERT: F 70 THR cc_start: 0.8437 (p) cc_final: 0.8138 (p) REVERT: F 80 GLN cc_start: 0.8450 (tt0) cc_final: 0.7948 (tt0) REVERT: G 40 PHE cc_start: 0.8199 (m-10) cc_final: 0.7810 (m-80) REVERT: G 46 LYS cc_start: 0.8964 (ptpt) cc_final: 0.8648 (ptpp) REVERT: G 53 ASP cc_start: 0.8399 (p0) cc_final: 0.7217 (p0) REVERT: G 80 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7821 (tm-30) REVERT: H 39 GLN cc_start: 0.8219 (tt0) cc_final: 0.7384 (mt0) REVERT: H 46 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8208 (ptpt) REVERT: H 53 ASP cc_start: 0.8238 (p0) cc_final: 0.7322 (p0) outliers start: 12 outliers final: 8 residues processed: 185 average time/residue: 0.1330 time to fit residues: 33.5225 Evaluate side-chains 176 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain D 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5600 Z= 0.366 Angle : 0.852 10.511 7600 Z= 0.410 Chirality : 0.045 0.156 792 Planarity : 0.006 0.046 1000 Dihedral : 5.969 24.867 792 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.71 % Favored : 83.29 % 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: -5.22 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 99 PHE 0.021 0.002 PHE G 40 TYR 0.018 0.002 TYR G 87 ARG 0.003 0.000 ARG B 25 *********************** 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 194 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 0.646 Fit side-chains REVERT: A 36 TRP cc_start: 0.8902 (t-100) cc_final: 0.8541 (t-100) REVERT: A 55 ARG cc_start: 0.8579 (ttm110) cc_final: 0.7966 (mtt90) REVERT: B 46 LYS cc_start: 0.8883 (ptpt) cc_final: 0.8540 (ptpp) REVERT: B 50 TYR cc_start: 0.8335 (t80) cc_final: 0.7990 (t80) REVERT: B 63 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8083 (t80) REVERT: C 40 PHE cc_start: 0.8472 (m-80) cc_final: 0.8269 (m-10) REVERT: C 53 ASP cc_start: 0.8490 (p0) cc_final: 0.8255 (p0) REVERT: C 67 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8490 (mttt) REVERT: C 82 GLU cc_start: 0.8495 (mp0) cc_final: 0.7897 (mp0) REVERT: D 53 ASP cc_start: 0.8620 (p0) cc_final: 0.7274 (p0) REVERT: D 63 PHE cc_start: 0.8428 (t80) cc_final: 0.7840 (t80) REVERT: D 80 GLN cc_start: 0.8588 (tt0) cc_final: 0.7635 (tt0) REVERT: D 82 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8293 (mp0) REVERT: E 36 TRP cc_start: 0.8841 (t-100) cc_final: 0.8176 (t-100) REVERT: E 46 LYS cc_start: 0.8879 (ptpt) cc_final: 0.8566 (ptpp) REVERT: E 53 ASP cc_start: 0.8544 (p0) cc_final: 0.7628 (p0) REVERT: F 63 PHE cc_start: 0.8662 (t80) cc_final: 0.8271 (t80) REVERT: F 70 THR cc_start: 0.8522 (p) cc_final: 0.8218 (p) REVERT: F 84 GLU cc_start: 0.8321 (mp0) cc_final: 0.8103 (mp0) REVERT: G 40 PHE cc_start: 0.8350 (m-80) cc_final: 0.8075 (m-80) REVERT: G 46 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8599 (ptpp) REVERT: G 53 ASP cc_start: 0.8519 (p0) cc_final: 0.7222 (p0) REVERT: G 62 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7567 (mtm-85) REVERT: G 80 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7963 (tm-30) REVERT: H 39 GLN cc_start: 0.8235 (tt0) cc_final: 0.7467 (mt0) REVERT: H 46 LYS cc_start: 0.8799 (ptpt) cc_final: 0.8156 (ptpt) outliers start: 17 outliers final: 11 residues processed: 186 average time/residue: 0.1492 time to fit residues: 36.5974 Evaluate side-chains 184 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LEU 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 7 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5600 Z= 0.352 Angle : 0.831 9.156 7600 Z= 0.404 Chirality : 0.044 0.142 792 Planarity : 0.006 0.044 1000 Dihedral : 5.953 25.581 792 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 3.30 % Allowed : 26.04 % Favored : 70.66 % 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: -5.22 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 92 PHE 0.021 0.002 PHE D 40 TYR 0.014 0.002 TYR G 87 ARG 0.003 0.000 ARG B 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 200 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.570 Fit side-chains REVERT: A 36 TRP cc_start: 0.8925 (t-100) cc_final: 0.8573 (t-100) REVERT: A 55 ARG cc_start: 0.8535 (ttm110) cc_final: 0.7800 (mtt90) REVERT: B 50 TYR cc_start: 0.8320 (t80) cc_final: 0.7849 (t80) REVERT: B 63 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8134 (t80) REVERT: C 40 PHE cc_start: 0.8485 (m-80) cc_final: 0.8270 (m-10) REVERT: C 53 ASP cc_start: 0.8482 (p0) cc_final: 0.8219 (p0) REVERT: C 67 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8475 (mttt) REVERT: C 82 GLU cc_start: 0.8538 (mp0) cc_final: 0.8024 (mp0) REVERT: D 53 ASP cc_start: 0.8538 (p0) cc_final: 0.7159 (p0) REVERT: D 63 PHE cc_start: 0.8398 (t80) cc_final: 0.7844 (t80) REVERT: E 36 TRP cc_start: 0.8840 (t-100) cc_final: 0.8266 (t-100) REVERT: E 46 LYS cc_start: 0.8824 (ptpt) cc_final: 0.8520 (ptpp) REVERT: E 53 ASP cc_start: 0.8533 (p0) cc_final: 0.7627 (p0) REVERT: F 63 PHE cc_start: 0.8629 (t80) cc_final: 0.8235 (t80) REVERT: F 70 THR cc_start: 0.8576 (p) cc_final: 0.8288 (p) REVERT: F 84 GLU cc_start: 0.8403 (mp0) cc_final: 0.8140 (mp0) REVERT: G 40 PHE cc_start: 0.8354 (m-80) cc_final: 0.8086 (m-80) REVERT: G 53 ASP cc_start: 0.8514 (p0) cc_final: 0.7190 (p0) REVERT: G 62 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7612 (mtm-85) REVERT: G 80 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7990 (tm-30) REVERT: H 39 GLN cc_start: 0.8250 (tt0) cc_final: 0.7642 (mt0) REVERT: H 46 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8246 (ptpt) REVERT: H 53 ASP cc_start: 0.8329 (p0) cc_final: 0.7546 (p0) outliers start: 19 outliers final: 12 residues processed: 191 average time/residue: 0.1492 time to fit residues: 37.5749 Evaluate side-chains 189 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 47 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 100 VAL 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 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5600 Z= 0.257 Angle : 0.791 9.354 7600 Z= 0.378 Chirality : 0.045 0.141 792 Planarity : 0.005 0.041 1000 Dihedral : 5.645 25.833 792 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 2.08 % Allowed : 27.60 % Favored : 70.31 % 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: -5.09 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 92 PHE 0.022 0.002 PHE D 40 TYR 0.013 0.001 TYR G 87 ARG 0.003 0.000 ARG B 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 192 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 0.615 Fit side-chains REVERT: A 36 TRP cc_start: 0.8873 (t-100) cc_final: 0.8529 (t-100) REVERT: A 55 ARG cc_start: 0.8505 (ttm110) cc_final: 0.7833 (mtt90) REVERT: B 53 ASP cc_start: 0.8569 (p0) cc_final: 0.7447 (p0) REVERT: B 63 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8119 (t80) REVERT: C 53 ASP cc_start: 0.8460 (p0) cc_final: 0.7055 (p0) REVERT: C 67 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8408 (mttt) REVERT: C 82 GLU cc_start: 0.8495 (mp0) cc_final: 0.8201 (mp0) REVERT: D 53 ASP cc_start: 0.8440 (p0) cc_final: 0.7135 (p0) REVERT: D 63 PHE cc_start: 0.8386 (t80) cc_final: 0.7934 (t80) REVERT: E 46 LYS cc_start: 0.8745 (ptpt) cc_final: 0.8424 (ptpp) REVERT: E 53 ASP cc_start: 0.8547 (p0) cc_final: 0.7318 (p0) REVERT: E 63 PHE cc_start: 0.8442 (t80) cc_final: 0.7891 (t80) REVERT: F 63 PHE cc_start: 0.8495 (t80) cc_final: 0.8049 (t80) REVERT: F 70 THR cc_start: 0.8587 (p) cc_final: 0.8298 (p) REVERT: F 84 GLU cc_start: 0.8382 (mp0) cc_final: 0.8079 (mp0) REVERT: G 40 PHE cc_start: 0.8364 (m-80) cc_final: 0.8035 (m-80) REVERT: G 46 LYS cc_start: 0.8937 (ptpt) cc_final: 0.8642 (ptpp) REVERT: G 53 ASP cc_start: 0.8484 (p0) cc_final: 0.7212 (p0) REVERT: G 62 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7594 (mtm-85) REVERT: G 80 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7958 (tm-30) REVERT: H 46 LYS cc_start: 0.8793 (ptpt) cc_final: 0.8348 (ptmt) REVERT: H 53 ASP cc_start: 0.8278 (p0) cc_final: 0.7511 (p0) outliers start: 12 outliers final: 9 residues processed: 185 average time/residue: 0.1239 time to fit residues: 30.7586 Evaluate side-chains 182 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 F residue 79 LEU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 100 VAL 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 66 optimal weight: 0.0470 chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5600 Z= 0.240 Angle : 0.784 8.816 7600 Z= 0.370 Chirality : 0.045 0.135 792 Planarity : 0.005 0.045 1000 Dihedral : 5.424 25.167 792 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.43 % Allowed : 27.78 % 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: -4.98 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 92 PHE 0.026 0.002 PHE G 40 TYR 0.011 0.001 TYR G 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 192 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8850 (t-100) cc_final: 0.8502 (t-100) REVERT: A 55 ARG cc_start: 0.8491 (ttm110) cc_final: 0.7741 (mtt90) REVERT: B 53 ASP cc_start: 0.8563 (p0) cc_final: 0.7481 (p0) REVERT: B 63 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8015 (t80) REVERT: B 76 VAL cc_start: 0.8910 (t) cc_final: 0.8531 (p) REVERT: C 53 ASP cc_start: 0.8418 (p0) cc_final: 0.7049 (p0) REVERT: C 63 PHE cc_start: 0.8540 (t80) cc_final: 0.8272 (t80) REVERT: C 67 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8401 (mttt) REVERT: C 82 GLU cc_start: 0.8572 (mp0) cc_final: 0.8278 (mp0) REVERT: C 88 TYR cc_start: 0.7906 (m-80) cc_final: 0.7397 (t80) REVERT: D 53 ASP cc_start: 0.8384 (p0) cc_final: 0.7090 (p0) REVERT: D 63 PHE cc_start: 0.8319 (t80) cc_final: 0.7931 (t80) REVERT: E 36 TRP cc_start: 0.8754 (t-100) cc_final: 0.8236 (t-100) REVERT: E 53 ASP cc_start: 0.8594 (p0) cc_final: 0.7407 (p0) REVERT: E 63 PHE cc_start: 0.8387 (t80) cc_final: 0.7848 (t80) REVERT: E 82 GLU cc_start: 0.8176 (mp0) cc_final: 0.7933 (mp0) REVERT: E 87 TYR cc_start: 0.8306 (t80) cc_final: 0.7995 (t80) REVERT: F 37 TYR cc_start: 0.8281 (t80) cc_final: 0.8014 (t80) REVERT: F 63 PHE cc_start: 0.8443 (t80) cc_final: 0.8063 (t80) REVERT: G 40 PHE cc_start: 0.8381 (m-80) cc_final: 0.8021 (m-80) REVERT: G 46 LYS cc_start: 0.8886 (ptpt) cc_final: 0.8585 (ptpp) REVERT: G 53 ASP cc_start: 0.8458 (p0) cc_final: 0.7286 (p0) REVERT: G 62 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7585 (mtm-85) REVERT: G 80 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7883 (tm-30) REVERT: H 46 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8360 (ptmt) REVERT: H 53 ASP cc_start: 0.8237 (p0) cc_final: 0.7511 (p0) outliers start: 14 outliers final: 9 residues processed: 184 average time/residue: 0.1372 time to fit residues: 33.5294 Evaluate side-chains 183 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 29 ILE 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 62 ARG Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 100 VAL 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 32 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 5600 Z= 0.538 Angle : 0.949 7.553 7600 Z= 0.471 Chirality : 0.047 0.144 792 Planarity : 0.006 0.044 1000 Dihedral : 6.392 27.379 792 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.38 % Favored : 80.62 % Rotamer: Outliers : 2.78 % Allowed : 28.12 % Favored : 69.10 % 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: -5.24 (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 0.019 0.003 TRP E 36 PHE 0.040 0.004 PHE G 40 TYR 0.018 0.002 TYR A 88 ARG 0.004 0.001 ARG B 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 186 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 36 TRP cc_start: 0.9112 (t-100) cc_final: 0.8804 (t-100) REVERT: A 53 ASP cc_start: 0.8510 (p0) cc_final: 0.7511 (p0) REVERT: A 82 GLU cc_start: 0.8246 (tt0) cc_final: 0.7845 (tm-30) REVERT: B 63 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 80 GLN cc_start: 0.8503 (tt0) cc_final: 0.8278 (mt0) REVERT: B 82 GLU cc_start: 0.8311 (mp0) cc_final: 0.8023 (mp0) REVERT: B 84 GLU cc_start: 0.8427 (mp0) cc_final: 0.7428 (mp0) REVERT: C 53 ASP cc_start: 0.8459 (p0) cc_final: 0.8256 (p0) REVERT: C 67 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8487 (mttt) REVERT: C 82 GLU cc_start: 0.8644 (mp0) cc_final: 0.8229 (mp0) REVERT: D 53 ASP cc_start: 0.8541 (p0) cc_final: 0.7022 (p0) REVERT: D 63 PHE cc_start: 0.8517 (t80) cc_final: 0.7805 (t80) REVERT: E 46 LYS cc_start: 0.8837 (ptpp) cc_final: 0.8526 (ptpp) REVERT: E 53 ASP cc_start: 0.8640 (p0) cc_final: 0.7748 (p0) REVERT: F 63 PHE cc_start: 0.8769 (t80) cc_final: 0.8444 (t80) REVERT: G 46 LYS cc_start: 0.8965 (ptpt) cc_final: 0.8680 (ptpp) REVERT: G 53 ASP cc_start: 0.8681 (p0) cc_final: 0.7376 (p0) REVERT: G 62 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7612 (mtm-85) REVERT: G 80 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7950 (tm-30) REVERT: H 46 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8103 (ptpt) REVERT: H 50 TYR cc_start: 0.8687 (t80) cc_final: 0.8284 (t80) outliers start: 16 outliers final: 9 residues processed: 176 average time/residue: 0.1485 time to fit residues: 34.5317 Evaluate side-chains 176 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 79 LEU 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 52 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.085849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.074271 restraints weight = 15512.944| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 4.44 r_work: 0.3743 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5600 Z= 0.252 Angle : 0.825 8.555 7600 Z= 0.392 Chirality : 0.046 0.155 792 Planarity : 0.005 0.039 1000 Dihedral : 5.694 25.689 792 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.56 % Allowed : 29.17 % 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: -5.04 (0.22), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.17), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 92 PHE 0.021 0.002 PHE D 40 TYR 0.012 0.001 TYR G 87 ARG 0.003 0.000 ARG B 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.82 seconds wall clock time: 31 minutes 16.46 seconds (1876.46 seconds total)