Starting phenix.real_space_refine on Sat Dec 9 06:10:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/12_2023/8f6r_28889.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/12_2023/8f6r_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_28889/12_2023/8f6r_28889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/12_2023/8f6r_28889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/12_2023/8f6r_28889.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6r_28889/12_2023/8f6r_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-1.21rc1-5172/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: 5.64, per 1000 atoms: 0.55 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: 4.06 Conformation dependent library (CDL) restraints added in 1.7 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: 0.90 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: 3.36 Time building geometry restraints manager: 4.37 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: 0.640 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: 2.820 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.220 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- 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 : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2480 time to fit residues: 121.0238 Evaluate side-chains 184 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6765 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8272 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10368 Z= 0.233 Angle : 0.618 9.866 14028 Z= 0.324 Chirality : 0.040 0.357 1662 Planarity : 0.004 0.039 1884 Dihedral : 3.386 13.167 1458 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.76 % Allowed : 14.29 % Favored : 82.95 % 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: 2.03 (0.21), residues: 1302 helix: 1.58 (0.13), residues: 1248 sheet: None (None), residues: 0 loop : -3.66 (0.55), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 201 PHE 0.025 0.003 PHE A 185 ARG 0.005 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 283 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 270 average time/residue: 0.2055 time to fit residues: 78.9375 Evaluate side-chains 211 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0945 time to fit residues: 5.3062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN D 164 GLN F 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10368 Z= 0.194 Angle : 0.584 10.513 14028 Z= 0.301 Chirality : 0.039 0.389 1662 Planarity : 0.004 0.034 1884 Dihedral : 3.369 12.341 1458 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.81 % Allowed : 18.10 % Favored : 80.10 % 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: 2.83 (0.22), residues: 1302 helix: 2.10 (0.14), residues: 1248 sheet: None (None), residues: 0 loop : -3.61 (0.63), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 201 PHE 0.018 0.002 PHE A 185 ARG 0.004 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 247 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 1.157 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 238 average time/residue: 0.2147 time to fit residues: 72.6128 Evaluate side-chains 201 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0927 time to fit residues: 3.2349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10368 Z= 0.204 Angle : 0.593 11.337 14028 Z= 0.303 Chirality : 0.039 0.408 1662 Planarity : 0.004 0.034 1884 Dihedral : 3.355 12.180 1458 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.71 % Allowed : 19.81 % Favored : 78.48 % 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: 2.96 (0.22), residues: 1302 helix: 2.18 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.17 (0.67), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 PHE 0.012 0.002 PHE F 185 ARG 0.003 0.000 ARG C 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 237 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 1.198 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 236 average time/residue: 0.1977 time to fit residues: 67.8286 Evaluate side-chains 199 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1689 time to fit residues: 2.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.0070 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN C 220 GLN D 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4125 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= 0.198 Angle : 0.640 12.338 14028 Z= 0.312 Chirality : 0.041 0.415 1662 Planarity : 0.003 0.033 1884 Dihedral : 3.403 11.968 1458 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.43 % Allowed : 20.38 % Favored : 78.19 % 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: 2.23 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.14 (0.68), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 PHE 0.012 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 233 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 218 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 227 average time/residue: 0.2118 time to fit residues: 70.7400 Evaluate side-chains 199 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0889 time to fit residues: 3.0415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN F 164 GLN F 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10368 Z= 0.201 Angle : 0.665 12.268 14028 Z= 0.323 Chirality : 0.042 0.405 1662 Planarity : 0.003 0.030 1884 Dihedral : 3.418 11.689 1458 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.29 % Allowed : 23.62 % Favored : 76.10 % 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: 3.04 (0.22), residues: 1302 helix: 2.22 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.13 (0.67), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 201 PHE 0.010 0.002 PHE F 185 ARG 0.001 0.000 ARG D 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 220 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 217 time to evaluate : 1.225 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 219 average time/residue: 0.2066 time to fit residues: 65.0058 Evaluate side-chains 188 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10368 Z= 0.196 Angle : 0.672 13.316 14028 Z= 0.328 Chirality : 0.042 0.413 1662 Planarity : 0.003 0.032 1884 Dihedral : 3.405 11.200 1458 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.24 % Allowed : 23.33 % Favored : 75.43 % 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: 2.98 (0.22), residues: 1302 helix: 2.21 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -5.79 (0.22), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 201 PHE 0.014 0.002 PHE C 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 230 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.231 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 224 average time/residue: 0.2043 time to fit residues: 65.4217 Evaluate side-chains 193 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0923 time to fit residues: 2.4851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10368 Z= 0.211 Angle : 0.680 13.678 14028 Z= 0.335 Chirality : 0.042 0.448 1662 Planarity : 0.003 0.032 1884 Dihedral : 3.403 11.814 1458 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.57 % Allowed : 23.71 % Favored : 75.71 % 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: 2.97 (0.22), residues: 1302 helix: 2.18 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.09 (0.68), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 201 PHE 0.009 0.002 PHE C 185 ARG 0.002 0.000 ARG C 139 *********************** 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 205 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.250 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 203 average time/residue: 0.2099 time to fit residues: 61.1602 Evaluate side-chains 189 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0948 time to fit residues: 2.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 220 GLN E 166 ASN E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10368 Z= 0.206 Angle : 0.674 13.661 14028 Z= 0.334 Chirality : 0.042 0.418 1662 Planarity : 0.003 0.032 1884 Dihedral : 3.400 11.361 1458 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.67 % Allowed : 23.81 % Favored : 75.52 % 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: 3.02 (0.22), residues: 1302 helix: 2.21 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.02 (0.70), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 201 PHE 0.007 0.002 PHE C 185 ARG 0.002 0.000 ARG E 139 *********************** 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 201 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 195 average time/residue: 0.1962 time to fit residues: 56.2255 Evaluate side-chains 189 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1107 time to fit residues: 2.0293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10368 Z= 0.211 Angle : 0.673 14.001 14028 Z= 0.338 Chirality : 0.041 0.449 1662 Planarity : 0.003 0.032 1884 Dihedral : 3.398 11.475 1458 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.29 % Allowed : 24.48 % Favored : 75.24 % 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: 3.01 (0.22), residues: 1302 helix: 2.20 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -3.96 (0.72), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 201 PHE 0.006 0.001 PHE B 185 ARG 0.001 0.000 ARG F 221 ********************** 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 198 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.372 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 197 average time/residue: 0.2041 time to fit residues: 58.4254 Evaluate side-chains 191 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0905 time to fit residues: 1.7053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.0270 chunk 14 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079614 restraints weight = 24377.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082886 restraints weight = 16529.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085198 restraints weight = 12663.452| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10368 Z= 0.203 Angle : 0.684 14.307 14028 Z= 0.340 Chirality : 0.041 0.442 1662 Planarity : 0.003 0.032 1884 Dihedral : 3.408 11.405 1458 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.29 % Allowed : 24.67 % 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: 2.98 (0.22), residues: 1302 helix: 2.20 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -5.74 (0.25), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 PHE 0.005 0.001 PHE B 185 ARG 0.001 0.000 ARG D 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.50 seconds wall clock time: 37 minutes 33.87 seconds (2253.87 seconds total)