Starting phenix.real_space_refine on Sun Mar 10 22:05:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/03_2024/6ic3_4452.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/03_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_4452/03_2024/6ic3_4452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/03_2024/6ic3_4452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/03_2024/6ic3_4452.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ic3_4452/03_2024/6ic3_4452.pdb" } 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 Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 25": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "H ARG 17": "NH1" <-> "NH2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5472 Number of models: 1 Model: "" Number of chains: 8 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} Chain: "B" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "C" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "E" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "F" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "G" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Time building chain proxies: 3.64, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 2.12 Conformation dependent library (CDL) restraints added in 916.6 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 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: 1.26 Time building geometry restraints manager: 2.36 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: 101.16 - 107.74: 373 107.74 - 114.32: 2816 114.32 - 120.90: 2463 120.90 - 127.48: 1876 127.48 - 134.06: 72 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 2.520 nonbonded pdb=" O THR H 70 " pdb=" OG1 THR H 70 " model vdw 2.306 2.440 nonbonded pdb=" O THR B 70 " pdb=" OG1 THR B 70 " model vdw 2.306 2.440 nonbonded pdb=" O THR F 70 " pdb=" OG1 THR F 70 " model vdw 2.307 2.440 nonbonded pdb=" O THR E 70 " pdb=" OG1 THR E 70 " model vdw 2.307 2.440 ... (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 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.750 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.990 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 5600 Z= 0.660 Angle : 1.262 8.957 7600 Z= 0.668 Chirality : 0.056 0.128 792 Planarity : 0.009 0.051 1000 Dihedral : 16.173 57.866 1960 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.85 % Favored : 83.15 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.19), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP F 99 PHE 0.020 0.005 PHE E 63 TYR 0.013 0.003 TYR D 50 ARG 0.001 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 227 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8805 (mttt) cc_final: 0.8293 (mtpt) REVERT: A 36 TRP cc_start: 0.8826 (t-100) cc_final: 0.8563 (t-100) REVERT: A 80 GLN cc_start: 0.8796 (tt0) cc_final: 0.8535 (tt0) REVERT: B 35 LYS cc_start: 0.8338 (mttt) cc_final: 0.7694 (ttmm) REVERT: B 36 TRP cc_start: 0.8876 (t-100) cc_final: 0.8423 (t-100) REVERT: B 37 TYR cc_start: 0.8376 (t80) cc_final: 0.7268 (t80) REVERT: B 50 TYR cc_start: 0.8478 (t80) cc_final: 0.8157 (t80) REVERT: B 80 GLN cc_start: 0.8619 (tt0) cc_final: 0.8009 (tt0) REVERT: C 40 PHE cc_start: 0.8537 (m-80) cc_final: 0.8273 (m-10) REVERT: C 46 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8809 (ptpt) REVERT: D 53 ASP cc_start: 0.8613 (p0) cc_final: 0.7869 (p0) REVERT: D 80 GLN cc_start: 0.8757 (tt0) cc_final: 0.8274 (tt0) REVERT: D 82 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 87 TYR cc_start: 0.8378 (t80) cc_final: 0.8068 (t80) REVERT: E 36 TRP cc_start: 0.8881 (t-100) cc_final: 0.8388 (t-100) REVERT: E 46 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8613 (ptpp) REVERT: E 80 GLN cc_start: 0.8605 (tt0) cc_final: 0.7975 (tt0) REVERT: E 87 TYR cc_start: 0.8327 (t80) cc_final: 0.8095 (t80) REVERT: F 36 TRP cc_start: 0.8781 (t-100) cc_final: 0.8530 (t-100) REVERT: F 50 TYR cc_start: 0.8498 (t80) cc_final: 0.8186 (t80) REVERT: G 40 PHE cc_start: 0.8521 (m-80) cc_final: 0.8290 (m-10) REVERT: G 46 LYS cc_start: 0.8945 (ptpt) cc_final: 0.8676 (ptpp) REVERT: G 80 GLN cc_start: 0.8735 (tt0) cc_final: 0.8205 (tm-30) REVERT: G 82 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7842 (mt-10) REVERT: G 84 GLU cc_start: 0.8245 (mp0) cc_final: 0.8018 (mp0) REVERT: G 87 TYR cc_start: 0.8457 (t80) cc_final: 0.8169 (t80) REVERT: H 46 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8781 (ptpt) outliers start: 8 outliers final: 3 residues processed: 235 average time/residue: 0.2296 time to fit residues: 65.4795 Evaluate side-chains 190 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5600 Z= 0.272 Angle : 0.793 8.145 7600 Z= 0.377 Chirality : 0.044 0.134 792 Planarity : 0.008 0.060 1000 Dihedral : 6.930 50.892 795 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.73 % Favored : 84.27 % Rotamer: Outliers : 5.03 % Allowed : 18.40 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.15), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 PHE 0.011 0.002 PHE D 101 TYR 0.016 0.002 TYR A 88 ARG 0.008 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 224 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8196 (tp) REVERT: A 35 LYS cc_start: 0.8743 (mttt) cc_final: 0.8202 (mtpt) REVERT: B 36 TRP cc_start: 0.8627 (t-100) cc_final: 0.8334 (t-100) REVERT: B 40 PHE cc_start: 0.8478 (m-10) cc_final: 0.8262 (m-10) REVERT: B 53 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 80 GLN cc_start: 0.8161 (tt0) cc_final: 0.7504 (tt0) REVERT: C 40 PHE cc_start: 0.8388 (m-80) cc_final: 0.8088 (m-10) REVERT: C 46 LYS cc_start: 0.8976 (ptpt) cc_final: 0.8742 (ptpt) REVERT: C 53 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8277 (p0) REVERT: C 67 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8395 (mttt) REVERT: C 101 PHE cc_start: 0.7088 (m-80) cc_final: 0.6664 (m-80) REVERT: D 40 PHE cc_start: 0.8338 (m-80) cc_final: 0.8134 (m-10) REVERT: D 53 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.7373 (p0) REVERT: D 80 GLN cc_start: 0.8401 (tt0) cc_final: 0.7732 (tt0) REVERT: D 82 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7955 (mt-10) REVERT: D 87 TYR cc_start: 0.8200 (t80) cc_final: 0.7850 (t80) REVERT: E 36 TRP cc_start: 0.8712 (t-100) cc_final: 0.8240 (t-100) REVERT: E 37 TYR cc_start: 0.8244 (t80) cc_final: 0.8029 (t80) REVERT: E 46 LYS cc_start: 0.8975 (ptpt) cc_final: 0.8679 (ptpp) REVERT: E 87 TYR cc_start: 0.8163 (t80) cc_final: 0.7947 (t80) REVERT: F 43 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8887 (m) REVERT: F 53 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8194 (p0) REVERT: G 36 TRP cc_start: 0.8612 (t-100) cc_final: 0.8390 (t-100) REVERT: G 46 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8500 (ptpp) REVERT: G 53 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.7716 (p0) REVERT: G 63 PHE cc_start: 0.8624 (t80) cc_final: 0.8348 (t80) REVERT: G 80 GLN cc_start: 0.8463 (tt0) cc_final: 0.8193 (tp40) REVERT: G 82 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7906 (mt-10) REVERT: H 37 TYR cc_start: 0.7610 (t80) cc_final: 0.7212 (t80) REVERT: H 40 PHE cc_start: 0.8503 (m-10) cc_final: 0.8216 (m-10) REVERT: H 46 LYS cc_start: 0.8951 (ptpt) cc_final: 0.8327 (ptpt) REVERT: H 50 TYR cc_start: 0.8601 (t80) cc_final: 0.8300 (t80) REVERT: H 53 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7840 (p0) outliers start: 29 outliers final: 8 residues processed: 207 average time/residue: 0.1504 time to fit residues: 41.2471 Evaluate side-chains 196 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F 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 53 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 53 ASP 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: 6.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5600 Z= 0.418 Angle : 0.863 7.172 7600 Z= 0.423 Chirality : 0.044 0.143 792 Planarity : 0.007 0.049 1000 Dihedral : 6.885 45.379 794 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.66 % Favored : 80.34 % Rotamer: Outliers : 3.99 % Allowed : 22.57 % Favored : 73.44 % 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: -5.33 (0.20), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 99 PHE 0.015 0.003 PHE G 40 TYR 0.025 0.002 TYR G 87 ARG 0.004 0.001 ARG B 31 *********************** 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 214 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 0.668 Fit side-chains REVERT: A 35 LYS cc_start: 0.8676 (mttt) cc_final: 0.8206 (mtpt) REVERT: A 88 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: B 36 TRP cc_start: 0.8839 (t-100) cc_final: 0.8363 (t-100) REVERT: B 50 TYR cc_start: 0.8303 (t80) cc_final: 0.8005 (t80) REVERT: C 40 PHE cc_start: 0.8431 (m-80) cc_final: 0.8124 (m-10) REVERT: C 46 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8738 (ptpt) REVERT: D 80 GLN cc_start: 0.8599 (tt0) cc_final: 0.8101 (tt0) REVERT: D 82 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8048 (mt-10) REVERT: E 36 TRP cc_start: 0.8829 (t-100) cc_final: 0.8227 (t-100) REVERT: E 46 LYS cc_start: 0.8943 (ptpt) cc_final: 0.8644 (ptpp) REVERT: E 87 TYR cc_start: 0.8281 (t80) cc_final: 0.8067 (t80) REVERT: F 53 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8514 (p0) REVERT: G 36 TRP cc_start: 0.8841 (t-100) cc_final: 0.8532 (t-100) REVERT: G 46 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8561 (ptpp) REVERT: G 80 GLN cc_start: 0.8567 (tt0) cc_final: 0.8306 (tp40) REVERT: G 82 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7943 (mt-10) REVERT: G 86 ASP cc_start: 0.8089 (m-30) cc_final: 0.7814 (m-30) REVERT: H 36 TRP cc_start: 0.8713 (t-100) cc_final: 0.8489 (t-100) REVERT: H 50 TYR cc_start: 0.8595 (t80) cc_final: 0.8347 (t80) REVERT: H 53 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8170 (p0) outliers start: 23 outliers final: 13 residues processed: 200 average time/residue: 0.1445 time to fit residues: 38.7867 Evaluate side-chains 195 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F 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 53 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 53 ASP 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: 3.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3435 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 : 0.816 7.758 7600 Z= 0.396 Chirality : 0.044 0.182 792 Planarity : 0.006 0.049 1000 Dihedral : 6.405 35.261 794 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.85 % Favored : 83.15 % Rotamer: Outliers : 3.47 % Allowed : 23.44 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.20), 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 TRP 0.018 0.002 TRP H 99 PHE 0.012 0.002 PHE A 40 TYR 0.033 0.002 TYR B 87 ARG 0.003 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 206 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 0.649 Fit side-chains REVERT: A 35 LYS cc_start: 0.8728 (mttt) cc_final: 0.8193 (mtpt) REVERT: A 88 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: B 50 TYR cc_start: 0.8293 (t80) cc_final: 0.7971 (t80) REVERT: C 40 PHE cc_start: 0.8435 (m-80) cc_final: 0.8131 (m-10) REVERT: C 46 LYS cc_start: 0.8978 (ptpt) cc_final: 0.8731 (ptpt) REVERT: C 87 TYR cc_start: 0.8366 (t80) cc_final: 0.7909 (t80) REVERT: D 80 GLN cc_start: 0.8544 (tt0) cc_final: 0.8232 (tt0) REVERT: D 82 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8164 (mt-10) REVERT: E 36 TRP cc_start: 0.8768 (t-100) cc_final: 0.8176 (t-100) REVERT: E 46 LYS cc_start: 0.8870 (ptpt) cc_final: 0.8576 (ptpp) REVERT: E 84 GLU cc_start: 0.8531 (mp0) cc_final: 0.8291 (mp0) REVERT: E 87 TYR cc_start: 0.8224 (t80) cc_final: 0.8023 (t80) REVERT: G 36 TRP cc_start: 0.8828 (t-100) cc_final: 0.8558 (t-100) REVERT: G 40 PHE cc_start: 0.8277 (m-10) cc_final: 0.7989 (m-10) REVERT: G 46 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8568 (ptpp) REVERT: G 71 SER cc_start: 0.8283 (p) cc_final: 0.7926 (m) REVERT: G 80 GLN cc_start: 0.8582 (tt0) cc_final: 0.8170 (tp40) REVERT: G 82 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7925 (mt-10) REVERT: G 86 ASP cc_start: 0.8043 (m-30) cc_final: 0.7842 (m-30) REVERT: G 87 TYR cc_start: 0.8400 (t80) cc_final: 0.8184 (t80) REVERT: H 36 TRP cc_start: 0.8680 (t-100) cc_final: 0.8454 (t-100) REVERT: H 39 GLN cc_start: 0.8209 (tt0) cc_final: 0.7623 (mt0) REVERT: H 46 LYS cc_start: 0.8734 (ptpt) cc_final: 0.8144 (ptpt) REVERT: H 53 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8162 (p0) outliers start: 20 outliers final: 12 residues processed: 192 average time/residue: 0.1438 time to fit residues: 36.7377 Evaluate side-chains 195 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 53 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E 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 79 LEU Chi-restraints excluded: chain H residue 53 ASP 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: 0.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 5600 Z= 0.484 Angle : 0.897 7.791 7600 Z= 0.444 Chirality : 0.045 0.225 792 Planarity : 0.006 0.044 1000 Dihedral : 6.764 28.718 793 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.79 % Favored : 79.21 % Rotamer: Outliers : 3.65 % Allowed : 26.74 % Favored : 69.62 % 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: -5.50 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP H 99 PHE 0.013 0.003 PHE A 40 TYR 0.032 0.002 TYR B 87 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 0.628 Fit side-chains REVERT: A 35 LYS cc_start: 0.8743 (mttt) cc_final: 0.8221 (mtpt) REVERT: A 88 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7418 (m-10) REVERT: B 50 TYR cc_start: 0.8273 (t80) cc_final: 0.7857 (t80) REVERT: C 40 PHE cc_start: 0.8509 (m-80) cc_final: 0.8262 (m-10) REVERT: C 87 TYR cc_start: 0.8435 (t80) cc_final: 0.7891 (t80) REVERT: D 80 GLN cc_start: 0.8580 (tt0) cc_final: 0.7660 (tt0) REVERT: D 82 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7928 (mp0) REVERT: E 36 TRP cc_start: 0.8941 (t-100) cc_final: 0.8605 (t-100) REVERT: E 46 LYS cc_start: 0.8924 (ptpt) cc_final: 0.8619 (ptpp) REVERT: G 46 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8572 (ptpp) REVERT: G 80 GLN cc_start: 0.8611 (tt0) cc_final: 0.8343 (tp40) REVERT: G 82 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8017 (mt-10) REVERT: G 86 ASP cc_start: 0.8081 (m-30) cc_final: 0.7873 (m-30) REVERT: H 36 TRP cc_start: 0.8837 (t-100) cc_final: 0.8518 (t-100) REVERT: H 46 LYS cc_start: 0.8672 (ptpt) cc_final: 0.8196 (ptpt) outliers start: 21 outliers final: 14 residues processed: 185 average time/residue: 0.1417 time to fit residues: 35.1486 Evaluate side-chains 185 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 B residue 53 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5600 Z= 0.345 Angle : 0.827 7.824 7600 Z= 0.401 Chirality : 0.044 0.187 792 Planarity : 0.006 0.048 1000 Dihedral : 6.303 25.647 792 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.57 % Favored : 83.43 % Rotamer: Outliers : 4.51 % Allowed : 26.39 % 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: -5.49 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 92 PHE 0.012 0.002 PHE H 40 TYR 0.029 0.002 TYR B 87 ARG 0.004 0.000 ARG D 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 204 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 0.647 Fit side-chains REVERT: A 35 LYS cc_start: 0.8699 (mttt) cc_final: 0.8181 (mtpt) REVERT: A 55 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8008 (mtt90) REVERT: A 88 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: B 50 TYR cc_start: 0.8276 (t80) cc_final: 0.7896 (t80) REVERT: B 63 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8073 (t80) REVERT: C 40 PHE cc_start: 0.8452 (m-80) cc_final: 0.8213 (m-10) REVERT: C 53 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8533 (p0) REVERT: C 87 TYR cc_start: 0.8327 (t80) cc_final: 0.7787 (t80) REVERT: D 80 GLN cc_start: 0.8517 (tt0) cc_final: 0.8191 (tt0) REVERT: E 36 TRP cc_start: 0.8855 (t-100) cc_final: 0.8511 (t-100) REVERT: E 40 PHE cc_start: 0.8382 (m-80) cc_final: 0.8160 (m-10) REVERT: E 46 LYS cc_start: 0.8900 (ptpt) cc_final: 0.8582 (ptpp) REVERT: F 63 PHE cc_start: 0.8745 (t80) cc_final: 0.8448 (t80) REVERT: G 25 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7480 (ttt180) REVERT: G 46 LYS cc_start: 0.8924 (ptpt) cc_final: 0.8601 (ptpp) REVERT: G 71 SER cc_start: 0.8187 (p) cc_final: 0.7920 (m) REVERT: G 80 GLN cc_start: 0.8589 (tt0) cc_final: 0.8187 (tp40) REVERT: G 82 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8010 (mt-10) REVERT: H 46 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8276 (ptpt) outliers start: 26 outliers final: 16 residues processed: 188 average time/residue: 0.1438 time to fit residues: 36.4668 Evaluate side-chains 192 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 53 ASP Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 25 ARG Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 53 ASP 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: 2.9990 chunk 39 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5600 Z= 0.306 Angle : 0.810 7.744 7600 Z= 0.385 Chirality : 0.044 0.155 792 Planarity : 0.006 0.041 1000 Dihedral : 5.999 25.753 792 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.96 % Favored : 81.04 % Rotamer: Outliers : 3.30 % Allowed : 28.65 % Favored : 68.06 % 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: -5.39 (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 0.015 0.002 TRP B 92 PHE 0.015 0.002 PHE H 40 TYR 0.027 0.002 TYR B 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 : 0.678 Fit side-chains REVERT: A 55 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8011 (mtt90) REVERT: A 88 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 50 TYR cc_start: 0.8247 (t80) cc_final: 0.7882 (t80) REVERT: B 63 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8041 (t80) REVERT: C 40 PHE cc_start: 0.8487 (m-80) cc_final: 0.8260 (m-10) REVERT: C 53 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8471 (p0) REVERT: C 82 GLU cc_start: 0.8233 (mp0) cc_final: 0.7932 (mp0) REVERT: C 87 TYR cc_start: 0.8291 (t80) cc_final: 0.7770 (t80) REVERT: D 63 PHE cc_start: 0.8407 (t80) cc_final: 0.7887 (t80) REVERT: D 82 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7960 (mp0) REVERT: E 36 TRP cc_start: 0.8815 (t-100) cc_final: 0.8464 (t-100) REVERT: E 40 PHE cc_start: 0.8490 (m-80) cc_final: 0.8277 (m-10) REVERT: E 46 LYS cc_start: 0.8898 (ptpt) cc_final: 0.8597 (ptpp) REVERT: E 63 PHE cc_start: 0.8378 (t80) cc_final: 0.7965 (t80) REVERT: E 87 TYR cc_start: 0.8168 (t80) cc_final: 0.7945 (t80) REVERT: F 63 PHE cc_start: 0.8690 (t80) cc_final: 0.8323 (t80) REVERT: G 36 TRP cc_start: 0.8807 (t-100) cc_final: 0.8549 (t-100) REVERT: G 46 LYS cc_start: 0.8887 (ptpt) cc_final: 0.8577 (ptpp) REVERT: G 71 SER cc_start: 0.8177 (p) cc_final: 0.7963 (m) REVERT: G 80 GLN cc_start: 0.8506 (tt0) cc_final: 0.8172 (tp40) REVERT: G 82 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7967 (mt-10) REVERT: H 36 TRP cc_start: 0.8642 (t-100) cc_final: 0.8337 (t-100) REVERT: H 40 PHE cc_start: 0.8506 (m-80) cc_final: 0.8286 (m-80) REVERT: H 46 LYS cc_start: 0.8769 (ptpt) cc_final: 0.8159 (ptpt) outliers start: 19 outliers final: 13 residues processed: 188 average time/residue: 0.1360 time to fit residues: 34.8855 Evaluate side-chains 193 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 53 ASP Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E 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 53 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.0030 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5600 Z= 0.329 Angle : 0.821 7.593 7600 Z= 0.392 Chirality : 0.044 0.147 792 Planarity : 0.006 0.043 1000 Dihedral : 6.023 26.702 792 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.98 % Favored : 82.02 % Rotamer: Outliers : 3.47 % Allowed : 28.30 % Favored : 68.23 % 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: -5.40 (0.21), 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 TRP 0.014 0.002 TRP B 92 PHE 0.024 0.002 PHE A 63 TYR 0.028 0.002 TYR B 87 ARG 0.002 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 202 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 0.644 Fit side-chains REVERT: A 55 ARG cc_start: 0.8549 (ttm110) cc_final: 0.7853 (mtt-85) REVERT: A 88 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: B 50 TYR cc_start: 0.8240 (t80) cc_final: 0.7929 (t80) REVERT: B 63 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7933 (t80) REVERT: C 53 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (p0) REVERT: C 82 GLU cc_start: 0.8258 (mp0) cc_final: 0.7936 (mp0) REVERT: C 87 TYR cc_start: 0.8306 (t80) cc_final: 0.7738 (t80) REVERT: D 63 PHE cc_start: 0.8404 (t80) cc_final: 0.7868 (t80) REVERT: D 82 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7965 (mp0) REVERT: E 36 TRP cc_start: 0.8814 (t-100) cc_final: 0.8453 (t-100) REVERT: E 40 PHE cc_start: 0.8517 (m-80) cc_final: 0.8313 (m-10) REVERT: E 46 LYS cc_start: 0.8883 (ptpt) cc_final: 0.8585 (ptpp) REVERT: E 63 PHE cc_start: 0.8434 (t80) cc_final: 0.7980 (t80) REVERT: F 63 PHE cc_start: 0.8710 (t80) cc_final: 0.8319 (t80) REVERT: G 71 SER cc_start: 0.8149 (p) cc_final: 0.7928 (m) REVERT: G 80 GLN cc_start: 0.8534 (tt0) cc_final: 0.8191 (tp40) REVERT: G 82 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8022 (mt-10) REVERT: H 36 TRP cc_start: 0.8651 (t-100) cc_final: 0.8312 (t-100) REVERT: H 40 PHE cc_start: 0.8564 (m-80) cc_final: 0.8318 (m-80) REVERT: H 46 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8147 (ptpt) outliers start: 20 outliers final: 16 residues processed: 189 average time/residue: 0.1352 time to fit residues: 34.6458 Evaluate side-chains 195 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 70 THR 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 B residue 53 ASP Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E 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 53 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4224 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= 0.247 Angle : 0.782 8.814 7600 Z= 0.364 Chirality : 0.044 0.138 792 Planarity : 0.005 0.043 1000 Dihedral : 5.682 26.002 792 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.73 % Favored : 84.27 % Rotamer: Outliers : 2.95 % Allowed : 29.51 % Favored : 67.53 % 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: -5.25 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 92 PHE 0.015 0.002 PHE H 40 TYR 0.025 0.002 TYR B 87 ARG 0.002 0.000 ARG B 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 201 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 0.639 Fit side-chains REVERT: A 29 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 53 ASP cc_start: 0.8756 (p0) cc_final: 0.7758 (p0) REVERT: A 55 ARG cc_start: 0.8485 (ttm110) cc_final: 0.7309 (mtt-85) REVERT: A 88 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: B 50 TYR cc_start: 0.8196 (t80) cc_final: 0.7893 (t80) REVERT: B 63 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 82 GLU cc_start: 0.8433 (mp0) cc_final: 0.7698 (mp0) REVERT: C 53 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8504 (p0) REVERT: C 82 GLU cc_start: 0.8330 (mp0) cc_final: 0.7963 (mp0) REVERT: C 87 TYR cc_start: 0.8247 (t80) cc_final: 0.7571 (t80) REVERT: D 63 PHE cc_start: 0.8271 (t80) cc_final: 0.7852 (t80) REVERT: D 82 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7921 (mp0) REVERT: E 36 TRP cc_start: 0.8686 (t-100) cc_final: 0.8351 (t-100) REVERT: E 46 LYS cc_start: 0.8694 (ptpt) cc_final: 0.8445 (ptpp) REVERT: E 63 PHE cc_start: 0.8366 (t80) cc_final: 0.7775 (t80) REVERT: E 86 ASP cc_start: 0.7753 (m-30) cc_final: 0.7533 (m-30) REVERT: F 63 PHE cc_start: 0.8564 (t80) cc_final: 0.8205 (t80) REVERT: G 37 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7803 (t80) REVERT: G 46 LYS cc_start: 0.8904 (ptpt) cc_final: 0.8612 (ptpp) REVERT: G 80 GLN cc_start: 0.8431 (tt0) cc_final: 0.8109 (tp40) REVERT: G 82 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8017 (mt-10) REVERT: G 87 TYR cc_start: 0.8332 (t80) cc_final: 0.7904 (t80) REVERT: H 40 PHE cc_start: 0.8532 (m-80) cc_final: 0.8331 (m-80) REVERT: H 46 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8218 (ptpt) REVERT: H 88 TYR cc_start: 0.8141 (m-80) cc_final: 0.7671 (t80) outliers start: 17 outliers final: 12 residues processed: 188 average time/residue: 0.1367 time to fit residues: 34.9030 Evaluate side-chains 196 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 B residue 53 ASP Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 53 ASP 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 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4291 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= 0.319 Angle : 0.828 7.811 7600 Z= 0.393 Chirality : 0.044 0.131 792 Planarity : 0.005 0.042 1000 Dihedral : 5.829 26.722 792 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.70 % Favored : 82.30 % Rotamer: Outliers : 3.82 % Allowed : 29.17 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.23 (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 TRP 0.013 0.002 TRP B 92 PHE 0.040 0.003 PHE E 40 TYR 0.026 0.002 TYR G 87 ARG 0.002 0.000 ARG D 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 0.625 Fit side-chains REVERT: A 53 ASP cc_start: 0.8773 (p0) cc_final: 0.7674 (p0) REVERT: A 55 ARG cc_start: 0.8529 (ttm110) cc_final: 0.7340 (mtt-85) REVERT: A 88 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: B 50 TYR cc_start: 0.8208 (t80) cc_final: 0.7894 (t80) REVERT: B 63 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8012 (t80) REVERT: C 53 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8500 (p0) REVERT: C 82 GLU cc_start: 0.8354 (mp0) cc_final: 0.8015 (mp0) REVERT: C 87 TYR cc_start: 0.8302 (t80) cc_final: 0.7638 (t80) REVERT: D 63 PHE cc_start: 0.8389 (t80) cc_final: 0.7880 (t80) REVERT: D 82 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7953 (mp0) REVERT: E 36 TRP cc_start: 0.8790 (t-100) cc_final: 0.8434 (t-100) REVERT: E 46 LYS cc_start: 0.8781 (ptpt) cc_final: 0.8464 (ptpp) REVERT: E 63 PHE cc_start: 0.8402 (t80) cc_final: 0.7813 (t80) REVERT: F 63 PHE cc_start: 0.8645 (t80) cc_final: 0.8334 (t80) REVERT: G 37 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7305 (t80) REVERT: G 46 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8624 (ptpp) REVERT: G 80 GLN cc_start: 0.8502 (tt0) cc_final: 0.8163 (tp40) REVERT: G 82 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8014 (mt-10) REVERT: G 87 TYR cc_start: 0.8356 (t80) cc_final: 0.7858 (t80) REVERT: H 37 TYR cc_start: 0.7657 (t80) cc_final: 0.7244 (t80) REVERT: H 46 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8180 (ptpt) outliers start: 22 outliers final: 15 residues processed: 183 average time/residue: 0.1426 time to fit residues: 35.8885 Evaluate side-chains 194 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 B residue 53 ASP Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 53 ASP 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: 0.7980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.084200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.074097 restraints weight = 16149.279| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 4.10 r_work: 0.3699 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5600 Z= 0.329 Angle : 0.833 9.244 7600 Z= 0.397 Chirality : 0.045 0.141 792 Planarity : 0.005 0.053 1000 Dihedral : 5.969 26.741 792 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.15 % Favored : 83.85 % Rotamer: Outliers : 3.30 % Allowed : 29.69 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.21), residues: 712 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.16), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 92 PHE 0.042 0.003 PHE D 40 TYR 0.026 0.002 TYR G 87 ARG 0.002 0.000 ARG B 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.36 seconds wall clock time: 31 minutes 32.34 seconds (1892.34 seconds total)