Starting phenix.real_space_refine on Tue Mar 3 13:41:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ic3_4452/03_2026/6ic3_4452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ic3_4452/03_2026/6ic3_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2026/6ic3_4452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2026/6ic3_4452.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2026/6ic3_4452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ic3_4452/03_2026/6ic3_4452.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C, D, E, F, G, H Time building chain proxies: 0.77, per 1000 atoms: 0.14 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 B 22 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 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: 0.46 Conformation dependent library (CDL) restraints added in 428.1 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: 0.18 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: 1.15 Time building geometry restraints manager: 0.63 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: 0.01 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: 3.450 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.570 ------------------------------------------------------------------------------- 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 5608 Z= 0.469 Angle : 1.263 8.957 7616 Z= 0.669 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.001 0.000 ARG B 55 TYR 0.013 0.003 TYR D 50 PHE 0.020 0.005 PHE E 63 TRP 0.043 0.006 TRP F 99 Details of bonding type rmsd covalent geometry : bond 0.00973 ( 5600) covalent geometry : angle 1.26208 ( 7600) SS BOND : bond 0.01339 ( 8) SS BOND : angle 1.60469 ( 16) hydrogen bonds : bond 0.14707 ( 32) hydrogen bonds : angle 9.15383 ( 96) *********************** 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 : 0.209 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: 0.8536 (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: 0.7269 (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: 0.8274 (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: 0.8009 (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: 0.8386 (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: 0.7971 (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: 0.8528 (t-100) REVERT: F 50 TYR cc_start: 0.8498 (t80) cc_final: 0.8186 (t80) REVERT: F 82 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7927 (mp0) 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: 0.8187 (tm-30) REVERT: G 82 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7816 (mt-10) REVERT: G 84 GLU cc_start: 0.8244 (mp0) cc_final: 0.8017 (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: 0.0971 time to fit residues: 27.6378 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 : 0.199 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 97 ASN C 97 ASN D 97 ASN E 97 ASN F 97 ASN G 97 ASN H 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.088617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.077816 restraints weight = 14972.710| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.99 r_work: 0.3792 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5608 Z= 0.152 Angle : 0.799 8.172 7616 Z= 0.380 Chirality : 0.044 0.136 792 Planarity : 0.008 0.057 1000 Dihedral : 6.216 25.999 795 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 3.47 % Allowed : 19.44 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 55 TYR 0.016 0.002 TYR A 88 PHE 0.011 0.002 PHE D 101 TRP 0.015 0.002 TRP B 99 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5600) covalent geometry : angle 0.79833 ( 7600) SS BOND : bond 0.00266 ( 8) SS BOND : angle 1.21632 ( 16) hydrogen bonds : bond 0.01788 ( 32) hydrogen bonds : angle 4.58139 ( 96) *********************** 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 222 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 35 LYS cc_start: 0.8688 (mttt) cc_final: 0.8040 (mtpt) REVERT: A 53 ASP cc_start: 0.8837 (p0) cc_final: 0.8006 (p0) REVERT: A 88 TYR cc_start: 0.8456 (m-80) cc_final: 0.8170 (m-10) REVERT: B 17 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7404 (mtp-110) REVERT: B 40 PHE cc_start: 0.8681 (m-10) cc_final: 0.8476 (m-10) REVERT: B 50 TYR cc_start: 0.8260 (t80) cc_final: 0.7992 (t80) REVERT: B 53 ASP cc_start: 0.8734 (p0) cc_final: 0.7572 (p0) REVERT: B 80 GLN cc_start: 0.8853 (tt0) cc_final: 0.8317 (tt0) REVERT: B 84 GLU cc_start: 0.8016 (mp0) cc_final: 0.7794 (mp0) REVERT: C 17 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7974 (mtp180) REVERT: C 40 PHE cc_start: 0.8584 (m-80) cc_final: 0.8283 (m-10) REVERT: C 53 ASP cc_start: 0.8870 (p0) cc_final: 0.7577 (p0) REVERT: C 67 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8145 (mttt) REVERT: C 83 ASP cc_start: 0.8336 (t0) cc_final: 0.7979 (t0) REVERT: C 101 PHE cc_start: 0.6821 (m-80) cc_final: 0.6350 (m-80) REVERT: D 53 ASP cc_start: 0.8738 (p0) cc_final: 0.7476 (p0) REVERT: D 87 TYR cc_start: 0.8355 (t80) cc_final: 0.7620 (t80) REVERT: E 36 TRP cc_start: 0.8766 (t-100) cc_final: 0.8041 (t-100) REVERT: E 46 LYS cc_start: 0.8203 (ptpt) cc_final: 0.7915 (ptpp) REVERT: E 82 GLU cc_start: 0.8402 (mp0) cc_final: 0.7972 (mp0) REVERT: E 84 GLU cc_start: 0.7956 (mp0) cc_final: 0.7735 (mp0) REVERT: E 87 TYR cc_start: 0.8390 (t80) cc_final: 0.8028 (t80) REVERT: F 43 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8580 (m) REVERT: F 53 ASP cc_start: 0.8683 (p0) cc_final: 0.7845 (p0) REVERT: F 82 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7748 (mp0) REVERT: G 36 TRP cc_start: 0.8652 (t-100) cc_final: 0.8272 (t-100) REVERT: G 40 PHE cc_start: 0.8575 (m-80) cc_final: 0.8371 (m-10) REVERT: G 46 LYS cc_start: 0.8122 (ptpt) cc_final: 0.7854 (ptpp) REVERT: G 52 ASN cc_start: 0.8325 (t0) cc_final: 0.8066 (t0) REVERT: G 53 ASP cc_start: 0.8733 (p0) cc_final: 0.7524 (p0) REVERT: G 63 PHE cc_start: 0.8551 (t80) cc_final: 0.7905 (t80) REVERT: G 80 GLN cc_start: 0.8741 (tt0) cc_final: 0.8401 (tm-30) REVERT: G 82 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8116 (mt-10) REVERT: G 84 GLU cc_start: 0.7618 (mp0) cc_final: 0.7214 (mp0) REVERT: G 87 TYR cc_start: 0.8448 (t80) cc_final: 0.8141 (t80) REVERT: H 40 PHE cc_start: 0.8596 (m-10) cc_final: 0.8168 (m-10) REVERT: H 46 LYS cc_start: 0.8389 (ptpt) cc_final: 0.7815 (ptpt) REVERT: H 53 ASP cc_start: 0.8837 (p0) cc_final: 0.7949 (p0) REVERT: H 83 ASP cc_start: 0.7461 (t0) cc_final: 0.7222 (t0) outliers start: 20 outliers final: 4 residues processed: 211 average time/residue: 0.0643 time to fit residues: 18.0783 Evaluate side-chains 189 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain F residue 43 THR 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 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** 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 = 0.084506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.074534 restraints weight = 15298.435| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.95 r_work: 0.3757 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5608 Z= 0.183 Angle : 0.787 8.099 7616 Z= 0.376 Chirality : 0.043 0.132 792 Planarity : 0.006 0.048 1000 Dihedral : 5.800 22.690 792 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 1.39 % Allowed : 23.26 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.000 ARG B 25 TYR 0.017 0.001 TYR B 87 PHE 0.007 0.002 PHE A 40 TRP 0.017 0.002 TRP B 99 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 5600) covalent geometry : angle 0.78640 ( 7600) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.87462 ( 16) hydrogen bonds : bond 0.01507 ( 32) hydrogen bonds : angle 3.88270 ( 96) *********************** 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 205 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.242 Fit side-chains REVERT: A 29 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 35 LYS cc_start: 0.8643 (mttt) cc_final: 0.8097 (mtpt) REVERT: A 53 ASP cc_start: 0.8972 (p0) cc_final: 0.8035 (p0) REVERT: B 50 TYR cc_start: 0.8156 (t80) cc_final: 0.7863 (t80) REVERT: B 53 ASP cc_start: 0.8710 (p0) cc_final: 0.7394 (p0) REVERT: B 76 VAL cc_start: 0.8667 (t) cc_final: 0.8310 (p) REVERT: B 80 GLN cc_start: 0.8832 (tt0) cc_final: 0.8596 (mt0) REVERT: B 87 TYR cc_start: 0.8803 (t80) cc_final: 0.8565 (t80) REVERT: C 17 ARG cc_start: 0.8317 (mtt180) cc_final: 0.8099 (mtp180) REVERT: C 40 PHE cc_start: 0.8549 (m-80) cc_final: 0.8307 (m-10) REVERT: C 53 ASP cc_start: 0.8902 (p0) cc_final: 0.8643 (p0) REVERT: C 67 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8367 (mtmt) REVERT: C 82 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8155 (mp0) REVERT: C 101 PHE cc_start: 0.6869 (m-80) cc_final: 0.6633 (m-80) REVERT: D 53 ASP cc_start: 0.8842 (p0) cc_final: 0.7634 (p0) REVERT: D 82 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8089 (mp0) REVERT: E 35 LYS cc_start: 0.7708 (mttt) cc_final: 0.7118 (mtpt) REVERT: E 36 TRP cc_start: 0.8874 (t-100) cc_final: 0.8061 (t-100) REVERT: E 82 GLU cc_start: 0.8526 (mp0) cc_final: 0.8091 (mp0) REVERT: E 84 GLU cc_start: 0.7922 (mp0) cc_final: 0.7693 (mp0) REVERT: E 87 TYR cc_start: 0.8428 (t80) cc_final: 0.8095 (t80) REVERT: F 17 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7852 (mtp180) REVERT: F 43 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8619 (m) REVERT: F 82 GLU cc_start: 0.8684 (mt-10) cc_final: 0.7992 (mp0) REVERT: G 36 TRP cc_start: 0.8738 (t-100) cc_final: 0.8166 (t-100) REVERT: G 46 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8135 (ptpp) REVERT: G 52 ASN cc_start: 0.8270 (t0) cc_final: 0.7860 (t0) REVERT: G 53 ASP cc_start: 0.8792 (p0) cc_final: 0.7598 (p0) REVERT: G 82 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8334 (mt-10) REVERT: G 84 GLU cc_start: 0.7778 (mp0) cc_final: 0.7293 (mp0) REVERT: H 40 PHE cc_start: 0.8607 (m-10) cc_final: 0.8295 (m-10) REVERT: H 46 LYS cc_start: 0.8276 (ptpt) cc_final: 0.7895 (ptmt) REVERT: H 53 ASP cc_start: 0.8876 (p0) cc_final: 0.7945 (p0) REVERT: H 83 ASP cc_start: 0.7560 (t0) cc_final: 0.7296 (t0) outliers start: 8 outliers final: 4 residues processed: 199 average time/residue: 0.0577 time to fit residues: 15.6080 Evaluate side-chains 193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain F residue 43 THR 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 68 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.082143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.072319 restraints weight = 16798.631| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 4.00 r_work: 0.3583 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 5608 Z= 0.390 Angle : 0.945 7.458 7616 Z= 0.476 Chirality : 0.046 0.244 792 Planarity : 0.007 0.045 1000 Dihedral : 6.724 25.587 792 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.98 % Favored : 82.02 % Rotamer: Outliers : 1.91 % Allowed : 24.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.40 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 55 TYR 0.023 0.003 TYR F 88 PHE 0.015 0.003 PHE H 101 TRP 0.029 0.004 TRP H 99 Details of bonding type rmsd covalent geometry : bond 0.00837 ( 5600) covalent geometry : angle 0.94345 ( 7600) SS BOND : bond 0.00659 ( 8) SS BOND : angle 1.37283 ( 16) hydrogen bonds : bond 0.02608 ( 32) hydrogen bonds : angle 3.92666 ( 96) *********************** 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 194 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.165 Fit side-chains REVERT: A 35 LYS cc_start: 0.8631 (mttt) cc_final: 0.8034 (mtpt) REVERT: A 53 ASP cc_start: 0.8669 (p0) cc_final: 0.8311 (p0) REVERT: A 82 GLU cc_start: 0.8178 (tt0) cc_final: 0.7175 (tm-30) REVERT: B 50 TYR cc_start: 0.8076 (t80) cc_final: 0.7704 (t80) REVERT: B 79 LEU cc_start: 0.9123 (mm) cc_final: 0.8912 (mm) REVERT: B 80 GLN cc_start: 0.8952 (tt0) cc_final: 0.8676 (mt0) REVERT: B 84 GLU cc_start: 0.8013 (mp0) cc_final: 0.7596 (mp0) REVERT: C 40 PHE cc_start: 0.8648 (m-80) cc_final: 0.8376 (m-10) REVERT: C 53 ASP cc_start: 0.8753 (p0) cc_final: 0.8542 (p0) REVERT: C 67 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8458 (mtmt) REVERT: C 84 GLU cc_start: 0.8352 (mp0) cc_final: 0.7950 (mp0) REVERT: C 88 TYR cc_start: 0.8883 (m-80) cc_final: 0.8634 (m-80) REVERT: D 53 ASP cc_start: 0.8796 (p0) cc_final: 0.7499 (p0) REVERT: D 82 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8208 (mp0) REVERT: D 84 GLU cc_start: 0.8014 (mp0) cc_final: 0.7588 (mp0) REVERT: E 36 TRP cc_start: 0.8950 (t-100) cc_final: 0.8160 (t-100) REVERT: E 46 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7998 (ptpp) REVERT: E 82 GLU cc_start: 0.8464 (mp0) cc_final: 0.7973 (mp0) REVERT: E 86 ASP cc_start: 0.8413 (m-30) cc_final: 0.8122 (m-30) REVERT: F 82 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8102 (mp0) REVERT: F 88 TYR cc_start: 0.8835 (m-80) cc_final: 0.8530 (m-80) REVERT: G 46 LYS cc_start: 0.8222 (ptpt) cc_final: 0.7935 (ptpp) REVERT: G 53 ASP cc_start: 0.8678 (p0) cc_final: 0.7485 (p0) REVERT: G 82 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8420 (mt-10) REVERT: G 84 GLU cc_start: 0.7967 (mp0) cc_final: 0.7657 (mp0) REVERT: H 40 PHE cc_start: 0.8522 (m-10) cc_final: 0.8276 (m-10) REVERT: H 46 LYS cc_start: 0.7948 (ptpt) cc_final: 0.7359 (ptpt) REVERT: H 50 TYR cc_start: 0.8812 (t80) cc_final: 0.8578 (t80) outliers start: 11 outliers final: 7 residues processed: 187 average time/residue: 0.0583 time to fit residues: 14.9715 Evaluate side-chains 175 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 79 LEU 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 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.083392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.073706 restraints weight = 16282.919| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.91 r_work: 0.3672 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5608 Z= 0.200 Angle : 0.804 7.361 7616 Z= 0.391 Chirality : 0.045 0.156 792 Planarity : 0.006 0.046 1000 Dihedral : 6.093 23.817 792 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 2.08 % Allowed : 25.35 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.33 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.014 0.002 TYR B 87 PHE 0.015 0.002 PHE G 40 TRP 0.014 0.002 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 5600) covalent geometry : angle 0.80371 ( 7600) SS BOND : bond 0.00237 ( 8) SS BOND : angle 0.90629 ( 16) hydrogen bonds : bond 0.01544 ( 32) hydrogen bonds : angle 3.48582 ( 96) *********************** 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 197 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.211 Fit side-chains REVERT: A 35 LYS cc_start: 0.8601 (mttt) cc_final: 0.7977 (mtpt) REVERT: A 53 ASP cc_start: 0.8833 (p0) cc_final: 0.7903 (p0) REVERT: A 55 ARG cc_start: 0.8438 (ttm110) cc_final: 0.7096 (mtt-85) REVERT: A 88 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: B 50 TYR cc_start: 0.8120 (t80) cc_final: 0.7695 (t80) REVERT: B 53 ASP cc_start: 0.8574 (p0) cc_final: 0.8239 (p0) REVERT: B 76 VAL cc_start: 0.8611 (t) cc_final: 0.8248 (p) REVERT: B 80 GLN cc_start: 0.8952 (tt0) cc_final: 0.8674 (mt0) REVERT: C 40 PHE cc_start: 0.8564 (m-80) cc_final: 0.8172 (m-10) REVERT: C 53 ASP cc_start: 0.8703 (p0) cc_final: 0.8482 (p0) REVERT: C 67 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8302 (mttt) REVERT: C 82 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8024 (mp0) REVERT: C 84 GLU cc_start: 0.8339 (mp0) cc_final: 0.7800 (mp0) REVERT: D 40 PHE cc_start: 0.8736 (m-10) cc_final: 0.8375 (m-10) REVERT: D 53 ASP cc_start: 0.8680 (p0) cc_final: 0.7249 (p0) REVERT: D 63 PHE cc_start: 0.8635 (t80) cc_final: 0.7466 (t80) REVERT: D 82 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8055 (mp0) REVERT: D 84 GLU cc_start: 0.7972 (mp0) cc_final: 0.7580 (mp0) REVERT: E 36 TRP cc_start: 0.8809 (t-100) cc_final: 0.7995 (t-100) REVERT: E 53 ASP cc_start: 0.8597 (p0) cc_final: 0.7880 (p0) REVERT: E 63 PHE cc_start: 0.8573 (t80) cc_final: 0.7614 (t80) REVERT: E 82 GLU cc_start: 0.8429 (mp0) cc_final: 0.8004 (mp0) REVERT: E 86 ASP cc_start: 0.8474 (m-30) cc_final: 0.8229 (m-30) REVERT: F 17 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7812 (mtp180) REVERT: F 63 PHE cc_start: 0.8726 (t80) cc_final: 0.7960 (t80) REVERT: F 82 GLU cc_start: 0.8748 (mt-10) cc_final: 0.7987 (mp0) REVERT: F 86 ASP cc_start: 0.8150 (m-30) cc_final: 0.7918 (m-30) REVERT: G 36 TRP cc_start: 0.8734 (t-100) cc_final: 0.8238 (t-100) REVERT: G 40 PHE cc_start: 0.8491 (m-10) cc_final: 0.8203 (m-80) REVERT: G 46 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7940 (ptpp) REVERT: G 52 ASN cc_start: 0.8143 (t0) cc_final: 0.7791 (t0) REVERT: G 53 ASP cc_start: 0.8567 (p0) cc_final: 0.7373 (p0) REVERT: G 80 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7934 (tp-100) REVERT: G 82 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8011 (mp0) REVERT: G 84 GLU cc_start: 0.8105 (mp0) cc_final: 0.7665 (mp0) REVERT: G 87 TYR cc_start: 0.8343 (t80) cc_final: 0.7939 (t80) REVERT: H 40 PHE cc_start: 0.8641 (m-10) cc_final: 0.8399 (m-10) REVERT: H 46 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7434 (ptpt) REVERT: H 53 ASP cc_start: 0.8696 (p0) cc_final: 0.8399 (p0) outliers start: 12 outliers final: 9 residues processed: 189 average time/residue: 0.0583 time to fit residues: 15.1219 Evaluate side-chains 191 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C 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 76 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 80 GLN 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 5 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.084602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.074622 restraints weight = 15711.762| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.89 r_work: 0.3695 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5608 Z= 0.200 Angle : 0.807 8.071 7616 Z= 0.387 Chirality : 0.044 0.158 792 Planarity : 0.006 0.044 1000 Dihedral : 5.859 25.101 792 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.87 % Favored : 84.13 % Rotamer: Outliers : 2.60 % Allowed : 26.04 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.26 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.014 0.001 TYR G 87 PHE 0.013 0.002 PHE G 40 TRP 0.013 0.002 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5600) covalent geometry : angle 0.80641 ( 7600) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.92655 ( 16) hydrogen bonds : bond 0.01616 ( 32) hydrogen bonds : angle 3.48319 ( 96) *********************** 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 198 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.236 Fit side-chains REVERT: A 35 LYS cc_start: 0.8631 (mttt) cc_final: 0.8053 (mtpt) REVERT: A 53 ASP cc_start: 0.8875 (p0) cc_final: 0.7790 (p0) REVERT: A 55 ARG cc_start: 0.8505 (ttm110) cc_final: 0.7141 (mtt-85) REVERT: A 88 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 50 TYR cc_start: 0.8197 (t80) cc_final: 0.7808 (t80) REVERT: B 53 ASP cc_start: 0.8670 (p0) cc_final: 0.7229 (p0) REVERT: B 63 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7906 (t80) REVERT: C 40 PHE cc_start: 0.8683 (m-80) cc_final: 0.8294 (m-10) REVERT: C 53 ASP cc_start: 0.8763 (p0) cc_final: 0.7193 (p0) REVERT: C 67 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8354 (mttt) REVERT: C 82 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8135 (mp0) REVERT: C 84 GLU cc_start: 0.8394 (mp0) cc_final: 0.7835 (mp0) REVERT: D 40 PHE cc_start: 0.8767 (m-10) cc_final: 0.8475 (m-10) REVERT: D 53 ASP cc_start: 0.8682 (p0) cc_final: 0.7067 (p0) REVERT: D 63 PHE cc_start: 0.8706 (t80) cc_final: 0.7621 (t80) REVERT: D 82 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8145 (mp0) REVERT: D 84 GLU cc_start: 0.8133 (mp0) cc_final: 0.7668 (mp0) REVERT: E 36 TRP cc_start: 0.8896 (t-100) cc_final: 0.8072 (t-100) REVERT: E 53 ASP cc_start: 0.8706 (p0) cc_final: 0.8020 (p0) REVERT: E 63 PHE cc_start: 0.8688 (t80) cc_final: 0.7577 (t80) REVERT: E 82 GLU cc_start: 0.8527 (mp0) cc_final: 0.8098 (mp0) REVERT: E 84 GLU cc_start: 0.8122 (mp0) cc_final: 0.7922 (mp0) REVERT: E 86 ASP cc_start: 0.8550 (m-30) cc_final: 0.8174 (m-30) REVERT: F 17 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7880 (mtp180) REVERT: F 63 PHE cc_start: 0.8841 (t80) cc_final: 0.8044 (t80) REVERT: F 82 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8057 (mp0) REVERT: G 36 TRP cc_start: 0.8786 (t-100) cc_final: 0.8253 (t-100) REVERT: G 40 PHE cc_start: 0.8550 (m-10) cc_final: 0.8307 (m-80) REVERT: G 46 LYS cc_start: 0.8357 (ptpt) cc_final: 0.8093 (ptpp) REVERT: G 52 ASN cc_start: 0.8298 (t0) cc_final: 0.7973 (t0) REVERT: G 53 ASP cc_start: 0.8702 (p0) cc_final: 0.7450 (p0) REVERT: G 82 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8203 (mp0) REVERT: G 84 GLU cc_start: 0.8154 (mp0) cc_final: 0.7730 (mp0) REVERT: G 87 TYR cc_start: 0.8426 (t80) cc_final: 0.8223 (t80) REVERT: H 40 PHE cc_start: 0.8703 (m-10) cc_final: 0.8488 (m-10) REVERT: H 46 LYS cc_start: 0.8151 (ptpt) cc_final: 0.7597 (ptpt) REVERT: H 53 ASP cc_start: 0.8833 (p0) cc_final: 0.8540 (p0) outliers start: 15 outliers final: 10 residues processed: 190 average time/residue: 0.0640 time to fit residues: 16.4410 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 : 0.217 ------------------------------------------------------------------------------- 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 C 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.084577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.075462 restraints weight = 16293.511| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.73 r_work: 0.3749 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5608 Z= 0.170 Angle : 0.784 7.847 7616 Z= 0.370 Chirality : 0.044 0.168 792 Planarity : 0.005 0.041 1000 Dihedral : 5.646 24.966 792 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 2.43 % Allowed : 25.87 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.20), 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 ARG 0.002 0.000 ARG B 25 TYR 0.013 0.001 TYR G 87 PHE 0.013 0.002 PHE G 40 TRP 0.013 0.002 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5600) covalent geometry : angle 0.78379 ( 7600) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.99518 ( 16) hydrogen bonds : bond 0.01522 ( 32) hydrogen bonds : angle 3.42371 ( 96) *********************** 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 204 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.227 Fit side-chains REVERT: A 35 LYS cc_start: 0.8661 (mttt) cc_final: 0.8080 (mtpt) REVERT: A 53 ASP cc_start: 0.8882 (p0) cc_final: 0.7630 (p0) REVERT: A 55 ARG cc_start: 0.8542 (ttm110) cc_final: 0.7102 (mtt-85) REVERT: A 88 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: B 50 TYR cc_start: 0.8200 (t80) cc_final: 0.7823 (t80) REVERT: B 53 ASP cc_start: 0.8680 (p0) cc_final: 0.7119 (p0) REVERT: B 63 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7879 (t80) REVERT: B 80 GLN cc_start: 0.8997 (tt0) cc_final: 0.8624 (mt0) REVERT: C 40 PHE cc_start: 0.8670 (m-80) cc_final: 0.8199 (m-10) REVERT: C 53 ASP cc_start: 0.8778 (p0) cc_final: 0.7202 (p0) REVERT: C 67 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8445 (mtmt) REVERT: C 82 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8204 (mp0) REVERT: C 84 GLU cc_start: 0.8527 (mp0) cc_final: 0.7887 (mp0) REVERT: D 40 PHE cc_start: 0.8754 (m-10) cc_final: 0.8447 (m-10) REVERT: D 53 ASP cc_start: 0.8667 (p0) cc_final: 0.7058 (p0) REVERT: D 63 PHE cc_start: 0.8729 (t80) cc_final: 0.7774 (t80) REVERT: D 82 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8219 (mp0) REVERT: D 84 GLU cc_start: 0.8211 (mp0) cc_final: 0.7710 (mp0) REVERT: E 36 TRP cc_start: 0.8909 (t-100) cc_final: 0.8099 (t-100) REVERT: E 53 ASP cc_start: 0.8763 (p0) cc_final: 0.7706 (p0) REVERT: E 63 PHE cc_start: 0.8699 (t80) cc_final: 0.7596 (t80) REVERT: E 82 GLU cc_start: 0.8613 (mp0) cc_final: 0.8217 (mp0) REVERT: E 86 ASP cc_start: 0.8678 (m-30) cc_final: 0.8280 (m-30) REVERT: F 17 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7928 (mtp180) REVERT: F 49 ILE cc_start: 0.8980 (mp) cc_final: 0.8757 (mp) REVERT: F 63 PHE cc_start: 0.8800 (t80) cc_final: 0.7924 (t80) REVERT: F 82 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8081 (mp0) REVERT: G 36 TRP cc_start: 0.8778 (t-100) cc_final: 0.8255 (t-100) REVERT: G 40 PHE cc_start: 0.8587 (m-80) cc_final: 0.8366 (m-80) REVERT: G 46 LYS cc_start: 0.8464 (ptpt) cc_final: 0.8175 (ptpp) REVERT: G 52 ASN cc_start: 0.8326 (t0) cc_final: 0.8004 (t0) REVERT: G 53 ASP cc_start: 0.8717 (p0) cc_final: 0.7422 (p0) REVERT: G 82 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8161 (mp0) REVERT: G 84 GLU cc_start: 0.8184 (mp0) cc_final: 0.7659 (mp0) REVERT: H 39 GLN cc_start: 0.7998 (tt0) cc_final: 0.7533 (mt0) REVERT: H 40 PHE cc_start: 0.8717 (m-10) cc_final: 0.8510 (m-80) REVERT: H 46 LYS cc_start: 0.8336 (ptpt) cc_final: 0.7755 (ptpt) REVERT: H 53 ASP cc_start: 0.8834 (p0) cc_final: 0.7799 (p0) REVERT: H 83 ASP cc_start: 0.8101 (t0) cc_final: 0.7846 (t0) outliers start: 14 outliers final: 10 residues processed: 195 average time/residue: 0.0633 time to fit residues: 16.6262 Evaluate side-chains 196 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 C 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.081227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.071295 restraints weight = 16379.410| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 4.00 r_work: 0.3660 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5608 Z= 0.226 Angle : 0.820 7.819 7616 Z= 0.393 Chirality : 0.044 0.169 792 Planarity : 0.005 0.044 1000 Dihedral : 5.821 25.648 792 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.56 % Favored : 82.44 % Rotamer: Outliers : 2.78 % Allowed : 26.22 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.024 0.002 TYR G 87 PHE 0.013 0.002 PHE G 40 TRP 0.012 0.002 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 5600) covalent geometry : angle 0.81921 ( 7600) SS BOND : bond 0.00319 ( 8) SS BOND : angle 1.04089 ( 16) hydrogen bonds : bond 0.01907 ( 32) hydrogen bonds : angle 3.56302 ( 96) *********************** 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 201 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.190 Fit side-chains REVERT: A 35 LYS cc_start: 0.8533 (mttt) cc_final: 0.7948 (mtpt) REVERT: A 53 ASP cc_start: 0.8773 (p0) cc_final: 0.7786 (p0) REVERT: A 55 ARG cc_start: 0.8399 (ttm110) cc_final: 0.7395 (mtt-85) REVERT: A 88 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: B 50 TYR cc_start: 0.8103 (t80) cc_final: 0.7693 (t80) REVERT: B 63 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7789 (t80) REVERT: B 82 GLU cc_start: 0.8501 (mp0) cc_final: 0.8273 (mp0) REVERT: C 40 PHE cc_start: 0.8696 (m-80) cc_final: 0.8276 (m-10) REVERT: C 53 ASP cc_start: 0.8678 (p0) cc_final: 0.7226 (p0) REVERT: C 67 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8408 (mtmt) REVERT: C 82 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8011 (mp0) REVERT: C 84 GLU cc_start: 0.8387 (mp0) cc_final: 0.7709 (mp0) REVERT: D 40 PHE cc_start: 0.8723 (m-10) cc_final: 0.8448 (m-10) REVERT: D 53 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.6914 (p0) REVERT: D 63 PHE cc_start: 0.8649 (t80) cc_final: 0.7544 (t80) REVERT: D 82 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8222 (mp0) REVERT: D 84 GLU cc_start: 0.8131 (mp0) cc_final: 0.7570 (mp0) REVERT: E 53 ASP cc_start: 0.8577 (p0) cc_final: 0.7912 (p0) REVERT: E 63 PHE cc_start: 0.8588 (t80) cc_final: 0.7502 (t80) REVERT: E 82 GLU cc_start: 0.8519 (mp0) cc_final: 0.8097 (mp0) REVERT: E 86 ASP cc_start: 0.8631 (m-30) cc_final: 0.8245 (m-30) REVERT: F 17 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7800 (mtp180) REVERT: F 63 PHE cc_start: 0.8795 (t80) cc_final: 0.7989 (t80) REVERT: F 82 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8026 (mp0) REVERT: F 84 GLU cc_start: 0.7990 (mp0) cc_final: 0.7777 (mp0) REVERT: G 40 PHE cc_start: 0.8563 (m-80) cc_final: 0.8348 (m-80) REVERT: G 46 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7873 (ptpp) REVERT: G 53 ASP cc_start: 0.8654 (p0) cc_final: 0.7338 (p0) REVERT: G 82 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8426 (mt-10) REVERT: G 84 GLU cc_start: 0.8102 (mp0) cc_final: 0.7580 (mp0) REVERT: H 39 GLN cc_start: 0.7800 (tt0) cc_final: 0.7362 (mt0) REVERT: H 46 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7463 (ptpt) REVERT: H 53 ASP cc_start: 0.8696 (p0) cc_final: 0.8380 (p0) REVERT: H 83 ASP cc_start: 0.7712 (t0) cc_final: 0.7431 (t0) REVERT: H 84 GLU cc_start: 0.8549 (mp0) cc_final: 0.8344 (mp0) outliers start: 16 outliers final: 10 residues processed: 193 average time/residue: 0.0607 time to fit residues: 16.0040 Evaluate side-chains 193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 C residue 79 LEU Chi-restraints excluded: chain D residue 53 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.082566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.073195 restraints weight = 16245.684| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.86 r_work: 0.3707 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5608 Z= 0.197 Angle : 0.814 8.561 7616 Z= 0.388 Chirality : 0.045 0.160 792 Planarity : 0.005 0.040 1000 Dihedral : 5.781 26.245 792 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 2.26 % Allowed : 27.26 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.19 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 25 TYR 0.025 0.001 TYR G 87 PHE 0.011 0.002 PHE G 40 TRP 0.012 0.002 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5600) covalent geometry : angle 0.81288 ( 7600) SS BOND : bond 0.00328 ( 8) SS BOND : angle 1.15780 ( 16) hydrogen bonds : bond 0.01741 ( 32) hydrogen bonds : angle 3.48784 ( 96) *********************** 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 196 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8639 (mttt) cc_final: 0.7968 (mtpt) REVERT: A 53 ASP cc_start: 0.8870 (p0) cc_final: 0.7797 (p0) REVERT: A 55 ARG cc_start: 0.8463 (ttm110) cc_final: 0.7298 (mtt-85) REVERT: A 88 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: B 35 LYS cc_start: 0.8421 (mttt) cc_final: 0.7653 (ttmm) REVERT: B 50 TYR cc_start: 0.8179 (t80) cc_final: 0.7764 (t80) REVERT: B 53 ASP cc_start: 0.8616 (p0) cc_final: 0.8406 (p0) REVERT: B 63 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8006 (t80) REVERT: B 80 GLN cc_start: 0.8991 (tt0) cc_final: 0.8491 (mt0) REVERT: C 40 PHE cc_start: 0.8740 (m-80) cc_final: 0.8286 (m-10) REVERT: C 53 ASP cc_start: 0.8721 (p0) cc_final: 0.7254 (p0) REVERT: C 67 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8348 (mttt) REVERT: C 82 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8101 (mp0) REVERT: C 84 GLU cc_start: 0.8552 (mp0) cc_final: 0.7894 (mp0) REVERT: D 40 PHE cc_start: 0.8805 (m-80) cc_final: 0.8534 (m-10) REVERT: D 53 ASP cc_start: 0.8633 (p0) cc_final: 0.7017 (p0) REVERT: D 63 PHE cc_start: 0.8722 (t80) cc_final: 0.7691 (t80) REVERT: D 82 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8231 (mp0) REVERT: D 84 GLU cc_start: 0.8216 (mp0) cc_final: 0.7790 (mp0) REVERT: E 37 TYR cc_start: 0.8736 (t80) cc_final: 0.7253 (t80) REVERT: E 53 ASP cc_start: 0.8733 (p0) cc_final: 0.8091 (p0) REVERT: E 63 PHE cc_start: 0.8649 (t80) cc_final: 0.7662 (t80) REVERT: E 80 GLN cc_start: 0.9204 (mt0) cc_final: 0.8613 (mm-40) REVERT: E 82 GLU cc_start: 0.8661 (mp0) cc_final: 0.8089 (mp0) REVERT: E 86 ASP cc_start: 0.8747 (m-30) cc_final: 0.8335 (m-30) REVERT: F 17 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7907 (mtp180) REVERT: F 63 PHE cc_start: 0.8851 (t80) cc_final: 0.8083 (t80) REVERT: F 82 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8047 (mp0) REVERT: F 84 GLU cc_start: 0.8190 (mp0) cc_final: 0.7968 (mp0) REVERT: G 36 TRP cc_start: 0.8741 (t-100) cc_final: 0.8236 (t-100) REVERT: G 40 PHE cc_start: 0.8530 (m-80) cc_final: 0.8327 (m-80) REVERT: G 46 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8081 (ptpp) REVERT: G 53 ASP cc_start: 0.8724 (p0) cc_final: 0.7432 (p0) REVERT: G 82 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8146 (mp0) REVERT: G 84 GLU cc_start: 0.8211 (mp0) cc_final: 0.7694 (mp0) REVERT: G 87 TYR cc_start: 0.8451 (t80) cc_final: 0.8199 (t80) REVERT: H 37 TYR cc_start: 0.7569 (t80) cc_final: 0.6686 (t80) REVERT: H 46 LYS cc_start: 0.8348 (ptpt) cc_final: 0.7931 (ptmt) REVERT: H 53 ASP cc_start: 0.8812 (p0) cc_final: 0.8526 (p0) REVERT: H 83 ASP cc_start: 0.7864 (t0) cc_final: 0.7586 (t0) outliers start: 13 outliers final: 10 residues processed: 188 average time/residue: 0.0606 time to fit residues: 15.4734 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 : 0.211 ------------------------------------------------------------------------------- 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 C 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 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 28 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.082076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.072812 restraints weight = 16489.172| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.89 r_work: 0.3681 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5608 Z= 0.215 Angle : 0.831 8.205 7616 Z= 0.398 Chirality : 0.045 0.198 792 Planarity : 0.005 0.042 1000 Dihedral : 5.847 26.191 792 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Rotamer: Outliers : 2.43 % Allowed : 26.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.003 0.000 ARG C 31 TYR 0.026 0.002 TYR G 87 PHE 0.024 0.002 PHE G 40 TRP 0.016 0.002 TRP E 36 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 5600) covalent geometry : angle 0.83028 ( 7600) SS BOND : bond 0.00324 ( 8) SS BOND : angle 1.12514 ( 16) hydrogen bonds : bond 0.01870 ( 32) hydrogen bonds : angle 3.58784 ( 96) ********************** 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 198 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8638 (mttt) cc_final: 0.7962 (mtpt) REVERT: A 53 ASP cc_start: 0.8829 (p0) cc_final: 0.7756 (p0) REVERT: A 55 ARG cc_start: 0.8407 (ttm110) cc_final: 0.7120 (mtt-85) REVERT: A 88 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: B 35 LYS cc_start: 0.8484 (mttt) cc_final: 0.7705 (ttmm) REVERT: B 50 TYR cc_start: 0.8166 (t80) cc_final: 0.7753 (t80) REVERT: B 53 ASP cc_start: 0.8622 (p0) cc_final: 0.8259 (p0) REVERT: B 63 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8017 (t80) REVERT: B 80 GLN cc_start: 0.9038 (tt0) cc_final: 0.8542 (mt0) REVERT: C 40 PHE cc_start: 0.8731 (m-80) cc_final: 0.8286 (m-10) REVERT: C 53 ASP cc_start: 0.8745 (p0) cc_final: 0.7264 (p0) REVERT: C 67 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8362 (mttt) REVERT: C 82 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8083 (mp0) REVERT: C 84 GLU cc_start: 0.8526 (mp0) cc_final: 0.7823 (mp0) REVERT: D 40 PHE cc_start: 0.8813 (m-80) cc_final: 0.8541 (m-10) REVERT: D 53 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7234 (p0) REVERT: D 63 PHE cc_start: 0.8744 (t80) cc_final: 0.7712 (t80) REVERT: D 82 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8244 (mp0) REVERT: D 84 GLU cc_start: 0.8210 (mp0) cc_final: 0.7641 (mp0) REVERT: E 36 TRP cc_start: 0.9074 (t-100) cc_final: 0.8844 (t-100) REVERT: E 63 PHE cc_start: 0.8681 (t80) cc_final: 0.7713 (t80) REVERT: E 80 GLN cc_start: 0.9241 (mt0) cc_final: 0.8733 (mm-40) REVERT: E 82 GLU cc_start: 0.8676 (mp0) cc_final: 0.8068 (mp0) REVERT: E 84 GLU cc_start: 0.8237 (mp0) cc_final: 0.7999 (mp0) REVERT: E 86 ASP cc_start: 0.8764 (m-30) cc_final: 0.8385 (m-30) REVERT: F 17 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7892 (mtp180) REVERT: F 63 PHE cc_start: 0.8901 (t80) cc_final: 0.8181 (t80) REVERT: F 82 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8072 (mp0) REVERT: F 84 GLU cc_start: 0.8239 (mp0) cc_final: 0.7979 (mp0) REVERT: G 40 PHE cc_start: 0.8709 (m-80) cc_final: 0.8375 (m-80) REVERT: G 46 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8050 (ptpp) REVERT: G 53 ASP cc_start: 0.8785 (p0) cc_final: 0.7474 (p0) REVERT: G 82 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8118 (mp0) REVERT: G 84 GLU cc_start: 0.8242 (mp0) cc_final: 0.7718 (mp0) REVERT: G 87 TYR cc_start: 0.8426 (t80) cc_final: 0.8124 (t80) REVERT: H 37 TYR cc_start: 0.7558 (t80) cc_final: 0.6736 (t80) REVERT: H 40 PHE cc_start: 0.8573 (m-10) cc_final: 0.8182 (m-10) REVERT: H 53 ASP cc_start: 0.8828 (p0) cc_final: 0.8532 (p0) REVERT: H 83 ASP cc_start: 0.8018 (t0) cc_final: 0.7770 (t0) outliers start: 14 outliers final: 11 residues processed: 190 average time/residue: 0.0635 time to fit residues: 16.2358 Evaluate side-chains 196 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 43 THR Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 53 ASP 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 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 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.085512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.076188 restraints weight = 15956.081| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.80 r_work: 0.3733 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5608 Z= 0.140 Angle : 0.782 8.954 7616 Z= 0.365 Chirality : 0.045 0.153 792 Planarity : 0.005 0.040 1000 Dihedral : 5.419 24.923 792 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 1.74 % Allowed : 27.78 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.06 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.022 0.001 TYR G 87 PHE 0.018 0.001 PHE G 40 TRP 0.014 0.002 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5600) covalent geometry : angle 0.78225 ( 7600) SS BOND : bond 0.00060 ( 8) SS BOND : angle 0.89196 ( 16) hydrogen bonds : bond 0.01488 ( 32) hydrogen bonds : angle 3.32841 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.45 seconds wall clock time: 22 minutes 48.39 seconds (1368.39 seconds total)