Starting phenix.real_space_refine on Fri Mar 15 01:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/03_2024/8f6r_28889.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/03_2024/8f6r_28889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/03_2024/8f6r_28889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/03_2024/8f6r_28889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/03_2024/8f6r_28889.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/03_2024/8f6r_28889.pdb" } resolution = 4.0 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= 0.003 sd= 0.057 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 12 5.16 5 C 6348 2.51 5 N 1872 2.21 5 O 2058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 202": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain: "F" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Time building chain proxies: 6.09, per 1000 atoms: 0.59 Number of scatterers: 10290 At special positions: 0 Unit cell: (125.073, 129.349, 54.519, 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 12 16.00 O 2058 8.00 N 1872 7.00 C 6348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 96.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 85 Processing helix chain 'A' and resid 86 through 110 Processing helix chain 'A' and resid 113 through 141 Processing helix chain 'A' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 197 Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.940A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 Processing helix chain 'B' and resid 30 through 54 removed outlier: 4.073A pdb=" N LEU B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 85 Processing helix chain 'B' and resid 86 through 110 Processing helix chain 'B' and resid 113 through 141 Processing helix chain 'B' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 197 Processing helix chain 'B' and resid 198 through 220 removed outlier: 3.939A pdb=" N ARG B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 29 Processing helix chain 'C' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 85 Processing helix chain 'C' and resid 86 through 110 Processing helix chain 'C' and resid 113 through 141 Processing helix chain 'C' and resid 142 through 166 removed outlier: 3.543A pdb=" N ASN C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 197 Processing helix chain 'C' and resid 198 through 220 removed outlier: 3.940A pdb=" N ARG C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 29 Processing helix chain 'D' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 85 Processing helix chain 'D' and resid 86 through 110 Processing helix chain 'D' and resid 113 through 141 Processing helix chain 'D' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 197 Processing helix chain 'D' and resid 198 through 220 removed outlier: 3.939A pdb=" N ARG D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 29 Processing helix chain 'E' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 85 Processing helix chain 'E' and resid 86 through 110 Processing helix chain 'E' and resid 113 through 141 Processing helix chain 'E' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 197 Processing helix chain 'E' and resid 198 through 220 removed outlier: 3.939A pdb=" N ARG E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 29 Processing helix chain 'F' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 Processing helix chain 'F' and resid 86 through 110 Processing helix chain 'F' and resid 113 through 141 Processing helix chain 'F' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 197 Processing helix chain 'F' and resid 198 through 220 removed outlier: 3.940A pdb=" N ARG F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 3135 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: 3.30 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3786 1.34 - 1.46: 571 1.46 - 1.57: 5987 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 10368 Sorted by residual: bond pdb=" CB TRP C 52 " pdb=" CG TRP C 52 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 bond pdb=" CB TRP F 52 " pdb=" CG TRP F 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.64e+00 bond pdb=" CB TRP B 52 " pdb=" CG TRP B 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.62e+00 bond pdb=" CB TRP E 52 " pdb=" CG TRP E 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.58e+00 bond pdb=" CB TRP A 52 " pdb=" CG TRP A 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.57e+00 ... (remaining 10363 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.08: 156 106.08 - 113.04: 5848 113.04 - 120.01: 3571 120.01 - 126.97: 4381 126.97 - 133.93: 72 Bond angle restraints: 14028 Sorted by residual: angle pdb=" N SER B 58 " pdb=" CA SER B 58 " pdb=" C SER B 58 " ideal model delta sigma weight residual 111.28 120.16 -8.88 1.09e+00 8.42e-01 6.64e+01 angle pdb=" N SER A 58 " pdb=" CA SER A 58 " pdb=" C SER A 58 " ideal model delta sigma weight residual 111.28 120.16 -8.88 1.09e+00 8.42e-01 6.63e+01 angle pdb=" N SER D 58 " pdb=" CA SER D 58 " pdb=" C SER D 58 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.61e+01 angle pdb=" N SER C 58 " pdb=" CA SER C 58 " pdb=" C SER C 58 " ideal model delta sigma weight residual 111.28 120.13 -8.85 1.09e+00 8.42e-01 6.59e+01 angle pdb=" N SER F 58 " pdb=" CA SER F 58 " pdb=" C SER F 58 " ideal model delta sigma weight residual 111.28 120.12 -8.84 1.09e+00 8.42e-01 6.58e+01 ... (remaining 14023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.27: 5694 13.27 - 26.55: 690 26.55 - 39.82: 198 39.82 - 53.10: 42 53.10 - 66.37: 18 Dihedral angle restraints: 6642 sinusoidal: 2754 harmonic: 3888 Sorted by residual: dihedral pdb=" CA TRP E 52 " pdb=" C TRP E 52 " pdb=" N LEU E 53 " pdb=" CA LEU E 53 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP A 52 " pdb=" C TRP A 52 " pdb=" N LEU A 53 " pdb=" CA LEU A 53 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP F 52 " pdb=" C TRP F 52 " pdb=" N LEU F 53 " pdb=" CA LEU F 53 " ideal model delta harmonic sigma weight residual 180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1473 0.061 - 0.122: 164 0.122 - 0.183: 13 0.183 - 0.244: 6 0.244 - 0.305: 6 Chirality restraints: 1662 Sorted by residual: chirality pdb=" CA SER B 58 " pdb=" N SER B 58 " pdb=" C SER B 58 " pdb=" CB SER B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA SER F 58 " pdb=" N SER F 58 " pdb=" C SER F 58 " pdb=" CB SER F 58 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA SER D 58 " pdb=" N SER D 58 " pdb=" C SER D 58 " pdb=" CB SER D 58 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1659 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 86 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 87 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 86 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO E 87 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 86 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 87 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " -0.025 5.00e-02 4.00e+02 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 42 2.58 - 3.16: 9766 3.16 - 3.74: 17399 3.74 - 4.32: 20508 4.32 - 4.90: 33156 Nonbonded interactions: 80871 Sorted by model distance: nonbonded pdb=" OE2 GLU F 11 " pdb=" NH2 ARG F 15 " model vdw 1.997 2.520 nonbonded pdb=" OE2 GLU B 11 " pdb=" NH2 ARG B 15 " model vdw 1.998 2.520 nonbonded pdb=" OE2 GLU D 11 " pdb=" NH2 ARG D 15 " model vdw 1.998 2.520 nonbonded pdb=" OE2 GLU C 11 " pdb=" NH2 ARG C 15 " model vdw 1.998 2.520 nonbonded pdb=" OE2 GLU A 11 " pdb=" NH2 ARG A 15 " model vdw 1.998 2.520 ... (remaining 80866 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' } 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 group one per residue 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: 0.440 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: 2.800 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.840 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.005 0.051 10368 Z= 0.331 Angle : 0.751 8.883 14028 Z= 0.474 Chirality : 0.043 0.305 1662 Planarity : 0.005 0.044 1884 Dihedral : 12.985 66.374 4062 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.46 (0.20), residues: 1302 helix: -0.69 (0.13), residues: 1248 sheet: None (None), residues: 0 loop : -2.81 (0.56), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 52 PHE 0.002 0.000 PHE B 185 ARG 0.002 0.000 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 110 ASN cc_start: 0.8677 (m110) cc_final: 0.8269 (t0) REVERT: A 121 LYS cc_start: 0.9440 (mttt) cc_final: 0.9078 (mtpp) REVERT: A 142 ASP cc_start: 0.8086 (t0) cc_final: 0.7856 (t0) REVERT: A 183 ILE cc_start: 0.9127 (mt) cc_final: 0.8831 (tp) REVERT: B 121 LYS cc_start: 0.9445 (mttt) cc_final: 0.9042 (mtpp) REVERT: B 142 ASP cc_start: 0.8038 (t0) cc_final: 0.7561 (t0) REVERT: B 185 PHE cc_start: 0.8784 (t80) cc_final: 0.8562 (t80) REVERT: C 110 ASN cc_start: 0.8679 (m110) cc_final: 0.8089 (t0) REVERT: C 121 LYS cc_start: 0.9417 (mttt) cc_final: 0.9041 (mtpt) REVERT: C 142 ASP cc_start: 0.8128 (t0) cc_final: 0.7719 (t0) REVERT: C 183 ILE cc_start: 0.9199 (mt) cc_final: 0.8981 (tp) REVERT: C 185 PHE cc_start: 0.8818 (t80) cc_final: 0.8171 (t80) REVERT: D 12 GLU cc_start: 0.8658 (tp30) cc_final: 0.8448 (tp30) REVERT: D 110 ASN cc_start: 0.8653 (m110) cc_final: 0.8405 (m110) REVERT: D 121 LYS cc_start: 0.9431 (mttt) cc_final: 0.9120 (mtpp) REVERT: D 183 ILE cc_start: 0.9079 (mt) cc_final: 0.8811 (tp) REVERT: D 185 PHE cc_start: 0.8747 (t80) cc_final: 0.8460 (t80) REVERT: E 110 ASN cc_start: 0.8714 (m110) cc_final: 0.8275 (t0) REVERT: E 121 LYS cc_start: 0.9412 (mttt) cc_final: 0.9132 (mtpp) REVERT: E 142 ASP cc_start: 0.7971 (t0) cc_final: 0.7522 (t0) REVERT: E 183 ILE cc_start: 0.9170 (mt) cc_final: 0.8923 (tp) REVERT: F 110 ASN cc_start: 0.8649 (m110) cc_final: 0.8260 (t0) REVERT: F 121 LYS cc_start: 0.9451 (mttt) cc_final: 0.9048 (mtpt) REVERT: F 185 PHE cc_start: 0.9000 (t80) cc_final: 0.8268 (t80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2475 time to fit residues: 120.6905 Evaluate side-chains 205 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 117 ASN B 173 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 173 ASN D 173 ASN E 173 ASN ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10368 Z= 0.224 Angle : 0.602 9.915 14028 Z= 0.315 Chirality : 0.039 0.338 1662 Planarity : 0.004 0.037 1884 Dihedral : 3.360 13.080 1458 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.76 % Allowed : 13.14 % Favored : 84.10 % 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: 2.13 (0.21), residues: 1302 helix: 1.65 (0.13), residues: 1248 sheet: None (None), residues: 0 loop : -3.66 (0.56), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 201 PHE 0.024 0.002 PHE A 185 ARG 0.004 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8603 (m110) cc_final: 0.8043 (t0) REVERT: A 121 LYS cc_start: 0.9421 (mttt) cc_final: 0.9133 (mtpp) REVERT: A 142 ASP cc_start: 0.8063 (t0) cc_final: 0.7694 (t0) REVERT: A 152 LEU cc_start: 0.9339 (pp) cc_final: 0.8889 (tp) REVERT: A 190 LEU cc_start: 0.9258 (mt) cc_final: 0.8975 (mt) REVERT: B 118 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7962 (mt-10) REVERT: B 121 LYS cc_start: 0.9417 (mttt) cc_final: 0.9194 (mtpp) REVERT: B 142 ASP cc_start: 0.7867 (t0) cc_final: 0.7665 (t0) REVERT: B 164 GLN cc_start: 0.8493 (tt0) cc_final: 0.8228 (tt0) REVERT: C 110 ASN cc_start: 0.8702 (m110) cc_final: 0.8022 (t0) REVERT: C 121 LYS cc_start: 0.9401 (mttt) cc_final: 0.9129 (mtpt) REVERT: C 142 ASP cc_start: 0.8067 (t0) cc_final: 0.7806 (t0) REVERT: D 58 SER cc_start: 0.8742 (m) cc_final: 0.8303 (p) REVERT: D 110 ASN cc_start: 0.8468 (m110) cc_final: 0.7897 (t0) REVERT: D 121 LYS cc_start: 0.9424 (mttt) cc_final: 0.9151 (mtpp) REVERT: D 152 LEU cc_start: 0.9298 (pp) cc_final: 0.8898 (tp) REVERT: D 164 GLN cc_start: 0.8463 (tt0) cc_final: 0.8253 (tp-100) REVERT: D 188 MET cc_start: 0.9134 (mtp) cc_final: 0.8863 (mtp) REVERT: E 110 ASN cc_start: 0.8604 (m110) cc_final: 0.8052 (t0) REVERT: E 142 ASP cc_start: 0.7824 (t0) cc_final: 0.7542 (t0) REVERT: E 152 LEU cc_start: 0.9312 (pp) cc_final: 0.8815 (tp) REVERT: E 164 GLN cc_start: 0.8554 (tt0) cc_final: 0.8352 (tt0) REVERT: F 110 ASN cc_start: 0.8662 (m110) cc_final: 0.8039 (t0) REVERT: F 121 LYS cc_start: 0.9420 (mttt) cc_final: 0.9118 (mtpt) REVERT: F 142 ASP cc_start: 0.7732 (t0) cc_final: 0.7487 (t0) REVERT: F 185 PHE cc_start: 0.8780 (t80) cc_final: 0.8181 (t80) outliers start: 29 outliers final: 21 residues processed: 285 average time/residue: 0.2079 time to fit residues: 83.8349 Evaluate side-chains 233 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.0170 chunk 114 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10368 Z= 0.190 Angle : 0.576 10.636 14028 Z= 0.294 Chirality : 0.038 0.382 1662 Planarity : 0.004 0.032 1884 Dihedral : 3.323 12.518 1458 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.86 % Allowed : 17.81 % Favored : 79.33 % 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: 2.93 (0.22), residues: 1302 helix: 2.19 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -3.73 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 PHE 0.017 0.003 PHE A 185 ARG 0.005 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8310 (mm-30) REVERT: A 58 SER cc_start: 0.8726 (m) cc_final: 0.8291 (p) REVERT: A 110 ASN cc_start: 0.8504 (m110) cc_final: 0.7835 (t0) REVERT: A 121 LYS cc_start: 0.9439 (mttt) cc_final: 0.9150 (mtpp) REVERT: A 142 ASP cc_start: 0.8101 (t0) cc_final: 0.7711 (t0) REVERT: A 178 LYS cc_start: 0.9311 (mttm) cc_final: 0.8942 (tppp) REVERT: A 196 ILE cc_start: 0.8932 (tp) cc_final: 0.8629 (tp) REVERT: B 118 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7903 (mt-10) REVERT: B 142 ASP cc_start: 0.7739 (t0) cc_final: 0.7460 (t0) REVERT: C 110 ASN cc_start: 0.8741 (m110) cc_final: 0.7983 (t0) REVERT: C 121 LYS cc_start: 0.9388 (mttt) cc_final: 0.9156 (mtpt) REVERT: C 142 ASP cc_start: 0.8041 (t0) cc_final: 0.7759 (t0) REVERT: C 152 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8917 (tt) REVERT: C 181 LYS cc_start: 0.9508 (ttmt) cc_final: 0.9295 (mmmt) REVERT: D 58 SER cc_start: 0.8676 (m) cc_final: 0.8184 (p) REVERT: D 121 LYS cc_start: 0.9424 (mttt) cc_final: 0.9161 (mtpp) REVERT: D 188 MET cc_start: 0.9141 (mtp) cc_final: 0.8767 (mtp) REVERT: E 110 ASN cc_start: 0.8587 (m110) cc_final: 0.7985 (t0) REVERT: E 142 ASP cc_start: 0.7747 (t0) cc_final: 0.7509 (t0) REVERT: E 164 GLN cc_start: 0.8602 (tt0) cc_final: 0.8384 (tt0) REVERT: E 183 ILE cc_start: 0.9096 (mt) cc_final: 0.8755 (tp) REVERT: F 110 ASN cc_start: 0.8619 (m110) cc_final: 0.7932 (t0) REVERT: F 118 GLU cc_start: 0.8613 (mm-30) cc_final: 0.7883 (mt-10) REVERT: F 121 LYS cc_start: 0.9446 (mttt) cc_final: 0.9187 (mtpt) REVERT: F 142 ASP cc_start: 0.7775 (t0) cc_final: 0.7535 (t0) REVERT: F 185 PHE cc_start: 0.8676 (t80) cc_final: 0.8090 (t80) outliers start: 30 outliers final: 18 residues processed: 261 average time/residue: 0.2008 time to fit residues: 75.3850 Evaluate side-chains 235 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN B 220 GLN E 164 GLN E 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10368 Z= 0.199 Angle : 0.584 11.574 14028 Z= 0.298 Chirality : 0.038 0.388 1662 Planarity : 0.003 0.029 1884 Dihedral : 3.318 12.300 1458 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.43 % Allowed : 18.95 % Favored : 77.62 % 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: 3.07 (0.22), residues: 1302 helix: 2.25 (0.14), residues: 1248 sheet: None (None), residues: 0 loop : -3.67 (0.63), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 201 PHE 0.007 0.002 PHE A 185 ARG 0.004 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 58 SER cc_start: 0.8792 (m) cc_final: 0.8296 (p) REVERT: A 121 LYS cc_start: 0.9465 (mttt) cc_final: 0.9203 (mtpp) REVERT: A 142 ASP cc_start: 0.8164 (t0) cc_final: 0.7714 (t0) REVERT: A 178 LYS cc_start: 0.9315 (mttm) cc_final: 0.8872 (tppp) REVERT: A 181 LYS cc_start: 0.9460 (tppt) cc_final: 0.9023 (mmtt) REVERT: A 196 ILE cc_start: 0.8984 (tp) cc_final: 0.8690 (tp) REVERT: B 142 ASP cc_start: 0.7751 (t0) cc_final: 0.7319 (t0) REVERT: C 79 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 110 ASN cc_start: 0.8686 (m110) cc_final: 0.7919 (t0) REVERT: C 121 LYS cc_start: 0.9428 (mttt) cc_final: 0.9190 (mtpp) REVERT: C 142 ASP cc_start: 0.8006 (t0) cc_final: 0.7700 (t0) REVERT: D 58 SER cc_start: 0.8797 (m) cc_final: 0.8316 (p) REVERT: D 121 LYS cc_start: 0.9429 (mttt) cc_final: 0.9199 (mtpp) REVERT: E 142 ASP cc_start: 0.7784 (t0) cc_final: 0.7448 (t0) REVERT: F 110 ASN cc_start: 0.8733 (m110) cc_final: 0.7821 (t0) REVERT: F 121 LYS cc_start: 0.9465 (mttt) cc_final: 0.9224 (mtpt) REVERT: F 142 ASP cc_start: 0.7594 (t0) cc_final: 0.7326 (t0) REVERT: F 185 PHE cc_start: 0.8689 (t80) cc_final: 0.8100 (t80) outliers start: 36 outliers final: 20 residues processed: 263 average time/residue: 0.1957 time to fit residues: 74.4008 Evaluate side-chains 235 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 0.0870 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN D 220 GLN F 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10368 Z= 0.201 Angle : 0.644 13.126 14028 Z= 0.309 Chirality : 0.040 0.396 1662 Planarity : 0.003 0.027 1884 Dihedral : 3.353 12.126 1458 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.10 % Allowed : 21.33 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.04 (0.22), residues: 1302 helix: 2.22 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.12 (0.69), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 PHE 0.016 0.002 PHE C 185 ARG 0.002 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8299 (mm-30) REVERT: A 58 SER cc_start: 0.8724 (m) cc_final: 0.8274 (p) REVERT: A 95 GLU cc_start: 0.8302 (tp30) cc_final: 0.8026 (tp30) REVERT: A 121 LYS cc_start: 0.9460 (mttt) cc_final: 0.9212 (mtpp) REVERT: A 142 ASP cc_start: 0.8198 (t0) cc_final: 0.7851 (t0) REVERT: A 178 LYS cc_start: 0.9310 (mttm) cc_final: 0.8853 (tppp) REVERT: A 181 LYS cc_start: 0.9436 (tppt) cc_final: 0.8975 (mmtt) REVERT: A 196 ILE cc_start: 0.8932 (tp) cc_final: 0.8640 (tp) REVERT: B 142 ASP cc_start: 0.7839 (t0) cc_final: 0.7377 (t0) REVERT: C 79 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 95 GLU cc_start: 0.8302 (tp30) cc_final: 0.8090 (tp30) REVERT: C 110 ASN cc_start: 0.8662 (m110) cc_final: 0.7852 (t0) REVERT: C 121 LYS cc_start: 0.9421 (mttt) cc_final: 0.9193 (mtpt) REVERT: C 142 ASP cc_start: 0.8052 (t0) cc_final: 0.7725 (t0) REVERT: D 58 SER cc_start: 0.8784 (m) cc_final: 0.8304 (p) REVERT: D 121 LYS cc_start: 0.9438 (mttt) cc_final: 0.9198 (mtpp) REVERT: D 188 MET cc_start: 0.8909 (mtp) cc_final: 0.8684 (mtp) REVERT: D 196 ILE cc_start: 0.8952 (tp) cc_final: 0.8685 (tp) REVERT: E 95 GLU cc_start: 0.8144 (tp30) cc_final: 0.7836 (tp30) REVERT: E 99 LEU cc_start: 0.8980 (mm) cc_final: 0.8547 (mm) REVERT: E 142 ASP cc_start: 0.7891 (t0) cc_final: 0.7483 (t0) REVERT: E 181 LYS cc_start: 0.9460 (mmtp) cc_final: 0.9036 (mmtt) REVERT: E 196 ILE cc_start: 0.8619 (tp) cc_final: 0.8408 (tp) REVERT: F 110 ASN cc_start: 0.8690 (m110) cc_final: 0.7799 (t0) REVERT: F 118 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8067 (mt-10) REVERT: F 121 LYS cc_start: 0.9458 (mttt) cc_final: 0.9223 (mtpt) REVERT: F 142 ASP cc_start: 0.7478 (t0) cc_final: 0.7203 (t0) outliers start: 22 outliers final: 15 residues processed: 247 average time/residue: 0.1978 time to fit residues: 70.3410 Evaluate side-chains 231 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN D 166 ASN F 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10368 Z= 0.205 Angle : 0.650 12.949 14028 Z= 0.314 Chirality : 0.040 0.408 1662 Planarity : 0.003 0.026 1884 Dihedral : 3.338 12.001 1458 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.10 % Allowed : 22.86 % Favored : 75.05 % 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: 3.03 (0.22), residues: 1302 helix: 2.22 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.10 (0.67), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 PHE 0.021 0.002 PHE F 185 ARG 0.001 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 228 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 58 SER cc_start: 0.8851 (m) cc_final: 0.8438 (p) REVERT: A 121 LYS cc_start: 0.9436 (mttt) cc_final: 0.9189 (mtpp) REVERT: A 142 ASP cc_start: 0.8170 (t0) cc_final: 0.7747 (t0) REVERT: A 178 LYS cc_start: 0.9288 (mttm) cc_final: 0.8770 (tppp) REVERT: A 181 LYS cc_start: 0.9435 (tppt) cc_final: 0.8988 (mmtt) REVERT: A 188 MET cc_start: 0.8825 (mtp) cc_final: 0.8604 (mtp) REVERT: A 196 ILE cc_start: 0.8917 (tp) cc_final: 0.8629 (tp) REVERT: B 121 LYS cc_start: 0.9381 (mtpp) cc_final: 0.9131 (mtpp) REVERT: B 142 ASP cc_start: 0.7806 (t0) cc_final: 0.7417 (t0) REVERT: C 79 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 110 ASN cc_start: 0.8594 (m110) cc_final: 0.7790 (t0) REVERT: C 142 ASP cc_start: 0.7852 (t0) cc_final: 0.7570 (t0) REVERT: C 164 GLN cc_start: 0.8635 (tt0) cc_final: 0.8327 (tp-100) REVERT: D 58 SER cc_start: 0.8799 (m) cc_final: 0.8324 (p) REVERT: D 121 LYS cc_start: 0.9442 (mttt) cc_final: 0.9200 (mtpp) REVERT: E 95 GLU cc_start: 0.8124 (tp30) cc_final: 0.7775 (tp30) REVERT: E 99 LEU cc_start: 0.8927 (mm) cc_final: 0.8464 (mm) REVERT: E 142 ASP cc_start: 0.7911 (t0) cc_final: 0.7485 (t0) REVERT: E 181 LYS cc_start: 0.9352 (mmtp) cc_final: 0.8953 (mmtt) REVERT: E 196 ILE cc_start: 0.8609 (tp) cc_final: 0.8395 (tp) REVERT: F 110 ASN cc_start: 0.8688 (m110) cc_final: 0.7781 (t0) REVERT: F 118 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8054 (mt-10) REVERT: F 142 ASP cc_start: 0.7590 (t0) cc_final: 0.7275 (t0) outliers start: 22 outliers final: 17 residues processed: 240 average time/residue: 0.2084 time to fit residues: 71.2087 Evaluate side-chains 232 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10368 Z= 0.200 Angle : 0.653 12.882 14028 Z= 0.316 Chirality : 0.040 0.396 1662 Planarity : 0.003 0.027 1884 Dihedral : 3.348 11.897 1458 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.71 % Allowed : 23.90 % Favored : 74.38 % 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: 3.10 (0.22), residues: 1302 helix: 2.26 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.08 (0.66), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 PHE 0.021 0.003 PHE F 185 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 58 SER cc_start: 0.8850 (m) cc_final: 0.8440 (p) REVERT: A 142 ASP cc_start: 0.8095 (t0) cc_final: 0.7719 (t0) REVERT: A 178 LYS cc_start: 0.9287 (mttm) cc_final: 0.8789 (tppp) REVERT: A 188 MET cc_start: 0.8785 (mtp) cc_final: 0.8576 (mtp) REVERT: A 196 ILE cc_start: 0.8868 (tp) cc_final: 0.8579 (tp) REVERT: B 142 ASP cc_start: 0.7760 (t0) cc_final: 0.7391 (t0) REVERT: C 79 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7530 (tm-30) REVERT: C 95 GLU cc_start: 0.8247 (tp30) cc_final: 0.7972 (tp30) REVERT: C 110 ASN cc_start: 0.8615 (m110) cc_final: 0.7796 (t0) REVERT: C 142 ASP cc_start: 0.7911 (t0) cc_final: 0.7557 (t0) REVERT: D 58 SER cc_start: 0.8858 (m) cc_final: 0.8390 (p) REVERT: D 121 LYS cc_start: 0.9442 (mttt) cc_final: 0.9201 (mtpp) REVERT: D 188 MET cc_start: 0.8946 (mtp) cc_final: 0.8725 (mtp) REVERT: E 95 GLU cc_start: 0.8090 (tp30) cc_final: 0.7783 (tp30) REVERT: E 99 LEU cc_start: 0.8924 (mm) cc_final: 0.8545 (mm) REVERT: E 142 ASP cc_start: 0.7911 (t0) cc_final: 0.7584 (t0) REVERT: E 181 LYS cc_start: 0.9375 (mmtp) cc_final: 0.8940 (mmtt) REVERT: E 182 LEU cc_start: 0.9288 (mt) cc_final: 0.8714 (tt) REVERT: E 196 ILE cc_start: 0.8729 (tp) cc_final: 0.8528 (tp) REVERT: F 110 ASN cc_start: 0.8770 (m110) cc_final: 0.7869 (t0) REVERT: F 142 ASP cc_start: 0.7511 (t0) cc_final: 0.7178 (t0) outliers start: 18 outliers final: 13 residues processed: 239 average time/residue: 0.1971 time to fit residues: 67.6996 Evaluate side-chains 229 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN C 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10368 Z= 0.209 Angle : 0.658 13.042 14028 Z= 0.322 Chirality : 0.040 0.402 1662 Planarity : 0.003 0.026 1884 Dihedral : 3.332 11.816 1458 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.00 % Allowed : 24.48 % Favored : 73.52 % 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: 3.08 (0.22), residues: 1302 helix: 2.25 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.02 (0.67), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 201 PHE 0.020 0.002 PHE F 185 ARG 0.001 0.000 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8672 (tp30) cc_final: 0.8450 (tp30) REVERT: A 16 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8440 (mm-30) REVERT: A 58 SER cc_start: 0.8821 (m) cc_final: 0.8391 (p) REVERT: A 142 ASP cc_start: 0.8020 (t0) cc_final: 0.7675 (t0) REVERT: A 178 LYS cc_start: 0.9275 (mttm) cc_final: 0.8773 (tppp) REVERT: A 188 MET cc_start: 0.8802 (mtp) cc_final: 0.8595 (mtp) REVERT: A 196 ILE cc_start: 0.8818 (tp) cc_final: 0.8532 (tp) REVERT: A 220 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: B 142 ASP cc_start: 0.7824 (t0) cc_final: 0.7437 (t0) REVERT: C 79 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 110 ASN cc_start: 0.8622 (m110) cc_final: 0.7792 (t0) REVERT: C 125 ILE cc_start: 0.9220 (mm) cc_final: 0.8919 (mm) REVERT: C 142 ASP cc_start: 0.7913 (t0) cc_final: 0.7555 (t0) REVERT: D 58 SER cc_start: 0.8864 (m) cc_final: 0.8412 (p) REVERT: D 121 LYS cc_start: 0.9436 (mttt) cc_final: 0.9232 (mtpp) REVERT: E 95 GLU cc_start: 0.8073 (tp30) cc_final: 0.7802 (tp30) REVERT: E 99 LEU cc_start: 0.8927 (mm) cc_final: 0.8561 (mm) REVERT: E 142 ASP cc_start: 0.7973 (t0) cc_final: 0.7616 (t0) REVERT: E 178 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8848 (tppp) REVERT: E 181 LYS cc_start: 0.9365 (mmtp) cc_final: 0.8932 (mmtt) REVERT: E 182 LEU cc_start: 0.9290 (mt) cc_final: 0.8711 (tt) REVERT: E 196 ILE cc_start: 0.8688 (tp) cc_final: 0.8487 (tp) REVERT: F 110 ASN cc_start: 0.8779 (m110) cc_final: 0.7937 (t0) REVERT: F 142 ASP cc_start: 0.7506 (t0) cc_final: 0.7177 (t0) REVERT: F 185 PHE cc_start: 0.8664 (t80) cc_final: 0.8094 (t80) outliers start: 21 outliers final: 15 residues processed: 245 average time/residue: 0.1972 time to fit residues: 70.0574 Evaluate side-chains 238 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10368 Z= 0.221 Angle : 0.670 13.347 14028 Z= 0.333 Chirality : 0.040 0.405 1662 Planarity : 0.003 0.026 1884 Dihedral : 3.330 11.848 1458 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.00 % Allowed : 24.57 % Favored : 73.43 % 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: 3.05 (0.22), residues: 1302 helix: 2.22 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -3.90 (0.70), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 201 PHE 0.020 0.003 PHE F 185 ARG 0.001 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8658 (tp30) cc_final: 0.8440 (tp30) REVERT: A 16 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8438 (mm-30) REVERT: A 58 SER cc_start: 0.8835 (m) cc_final: 0.8405 (p) REVERT: A 188 MET cc_start: 0.8863 (mtp) cc_final: 0.8603 (mtp) REVERT: A 196 ILE cc_start: 0.8830 (tp) cc_final: 0.8543 (tp) REVERT: A 220 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 142 ASP cc_start: 0.7935 (t0) cc_final: 0.7537 (t0) REVERT: C 79 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 125 ILE cc_start: 0.9283 (mm) cc_final: 0.8995 (mm) REVERT: C 142 ASP cc_start: 0.7869 (t0) cc_final: 0.7499 (t0) REVERT: D 58 SER cc_start: 0.8913 (m) cc_final: 0.8456 (p) REVERT: E 95 GLU cc_start: 0.8099 (tp30) cc_final: 0.7795 (tp30) REVERT: E 99 LEU cc_start: 0.8934 (mm) cc_final: 0.8549 (mm) REVERT: E 142 ASP cc_start: 0.8016 (t0) cc_final: 0.7628 (t0) REVERT: E 178 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8887 (tppp) REVERT: E 181 LYS cc_start: 0.9386 (mmtp) cc_final: 0.8953 (mmtt) REVERT: E 182 LEU cc_start: 0.9283 (mt) cc_final: 0.8735 (tt) REVERT: F 110 ASN cc_start: 0.8793 (m110) cc_final: 0.7937 (t0) REVERT: F 142 ASP cc_start: 0.7521 (t0) cc_final: 0.7203 (t0) REVERT: F 185 PHE cc_start: 0.8682 (t80) cc_final: 0.8080 (t80) outliers start: 21 outliers final: 16 residues processed: 233 average time/residue: 0.1914 time to fit residues: 64.5752 Evaluate side-chains 227 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN E 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10368 Z= 0.226 Angle : 0.680 13.517 14028 Z= 0.339 Chirality : 0.040 0.410 1662 Planarity : 0.003 0.026 1884 Dihedral : 3.332 11.950 1458 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 25.14 % Favored : 73.24 % 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: 3.04 (0.22), residues: 1302 helix: 2.22 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -3.83 (0.72), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 201 PHE 0.020 0.002 PHE F 185 ARG 0.001 0.000 ARG F 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8651 (tp30) cc_final: 0.8438 (tp30) REVERT: A 16 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8438 (mm-30) REVERT: A 58 SER cc_start: 0.8840 (m) cc_final: 0.8398 (p) REVERT: A 196 ILE cc_start: 0.8823 (tp) cc_final: 0.8536 (tp) REVERT: B 65 LYS cc_start: 0.9361 (ptmt) cc_final: 0.9100 (ptmm) REVERT: B 142 ASP cc_start: 0.7966 (t0) cc_final: 0.7559 (t0) REVERT: B 182 LEU cc_start: 0.9303 (mt) cc_final: 0.8630 (tt) REVERT: C 79 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 125 ILE cc_start: 0.9289 (mm) cc_final: 0.9000 (mm) REVERT: C 142 ASP cc_start: 0.7878 (t0) cc_final: 0.7504 (t0) REVERT: D 58 SER cc_start: 0.8912 (m) cc_final: 0.8453 (p) REVERT: E 95 GLU cc_start: 0.8100 (tp30) cc_final: 0.7788 (tp30) REVERT: E 99 LEU cc_start: 0.8936 (mm) cc_final: 0.8536 (mm) REVERT: E 142 ASP cc_start: 0.8022 (t0) cc_final: 0.7640 (t0) REVERT: E 178 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8901 (tppp) REVERT: E 182 LEU cc_start: 0.9280 (mt) cc_final: 0.8706 (tt) REVERT: F 110 ASN cc_start: 0.8790 (m110) cc_final: 0.7953 (t0) REVERT: F 142 ASP cc_start: 0.7568 (t0) cc_final: 0.7242 (t0) REVERT: F 185 PHE cc_start: 0.8663 (t80) cc_final: 0.8072 (t80) outliers start: 17 outliers final: 15 residues processed: 227 average time/residue: 0.1963 time to fit residues: 64.4343 Evaluate side-chains 227 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.105492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080024 restraints weight = 25052.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.083405 restraints weight = 16755.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085786 restraints weight = 12832.796| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10368 Z= 0.212 Angle : 0.699 13.999 14028 Z= 0.342 Chirality : 0.040 0.395 1662 Planarity : 0.003 0.026 1884 Dihedral : 3.351 11.688 1458 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.33 % Allowed : 26.00 % Favored : 72.67 % 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: 3.00 (0.22), residues: 1302 helix: 2.21 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -5.64 (0.23), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 201 PHE 0.019 0.003 PHE C 185 ARG 0.002 0.000 ARG B 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.65 seconds wall clock time: 36 minutes 50.73 seconds (2210.73 seconds total)