Starting phenix.real_space_refine (version: dev) on Fri May 13 14:44:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/05_2022/7p0z_13153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/05_2022/7p0z_13153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/05_2022/7p0z_13153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/05_2022/7p0z_13153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/05_2022/7p0z_13153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/05_2022/7p0z_13153.pdb" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.246 sd= 1.026 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 12873 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1839 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 14, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 7.90, per 1000 atoms: 0.61 Number of scatterers: 12873 At special positions: 0 Unit cell: (104.25, 103.416, 104.25, 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 42 16.00 O 2576 8.00 N 2247 7.00 C 8008 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: 5.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 75.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 80 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 223 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 80 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 165 Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 223 Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.554A pdb=" N ILE C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 80 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 166 through 171 removed outlier: 4.169A pdb=" N ARG C 169 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 223 Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 80 Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 223 Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 241 through 267 removed outlier: 4.460A pdb=" N LYS D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 80 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.168A pdb=" N ARG E 169 " --> pdb=" O ASP E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 223 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 241 through 267 removed outlier: 4.460A pdb=" N LYS E 247 " --> pdb=" O GLU E 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 80 Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 165 Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.169A pdb=" N ARG F 169 " --> pdb=" O ASP F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 223 Processing helix chain 'F' and resid 225 through 236 Processing helix chain 'F' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS F 247 " --> pdb=" O GLU F 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.553A pdb=" N ILE G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 80 Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 146 through 165 Processing helix chain 'G' and resid 166 through 171 removed outlier: 4.169A pdb=" N ARG G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 223 Processing helix chain 'G' and resid 225 through 236 Processing helix chain 'G' and resid 241 through 267 removed outlier: 4.461A pdb=" N LYS G 247 " --> pdb=" O GLU G 243 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2982 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: 3.65 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4008 1.33 - 1.44: 1633 1.44 - 1.56: 7393 1.56 - 1.68: 0 1.68 - 1.80: 77 Bond restraints: 13111 Sorted by residual: bond pdb=" CB ARG F 220 " pdb=" CG ARG F 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.83e+00 bond pdb=" CB ARG C 220 " pdb=" CG ARG C 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.80e+00 bond pdb=" CB ARG G 220 " pdb=" CG ARG G 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.80e+00 bond pdb=" CB ARG E 220 " pdb=" CG ARG E 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.72e+00 bond pdb=" CB ARG B 220 " pdb=" CG ARG B 220 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.70e+00 ... (remaining 13106 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.35: 301 105.35 - 112.51: 7056 112.51 - 119.68: 4423 119.68 - 126.84: 5868 126.84 - 134.01: 167 Bond angle restraints: 17815 Sorted by residual: angle pdb=" C ASN C 264 " pdb=" N THR C 265 " pdb=" CA THR C 265 " ideal model delta sigma weight residual 120.58 114.74 5.84 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C ASN F 264 " pdb=" N THR F 265 " pdb=" CA THR F 265 " ideal model delta sigma weight residual 120.58 114.74 5.84 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C ASN D 264 " pdb=" N THR D 265 " pdb=" CA THR D 265 " ideal model delta sigma weight residual 120.58 114.76 5.82 1.71e+00 3.42e-01 1.16e+01 angle pdb=" C ASN B 264 " pdb=" N THR B 265 " pdb=" CA THR B 265 " ideal model delta sigma weight residual 120.58 114.77 5.81 1.71e+00 3.42e-01 1.16e+01 angle pdb=" C ASN E 264 " pdb=" N THR E 265 " pdb=" CA THR E 265 " ideal model delta sigma weight residual 120.58 114.78 5.80 1.71e+00 3.42e-01 1.15e+01 ... (remaining 17810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 7420 16.61 - 33.22: 539 33.22 - 49.83: 77 49.83 - 66.44: 35 66.44 - 83.06: 42 Dihedral angle restraints: 8113 sinusoidal: 3241 harmonic: 4872 Sorted by residual: dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 -83.06 83.06 1 3.00e+01 1.11e-03 9.38e+00 dihedral pdb=" CB GLU C 270 " pdb=" CG GLU C 270 " pdb=" CD GLU C 270 " pdb=" OE1 GLU C 270 " ideal model delta sinusoidal sigma weight residual 0.00 -83.04 83.04 1 3.00e+01 1.11e-03 9.37e+00 dihedral pdb=" CB GLU E 270 " pdb=" CG GLU E 270 " pdb=" CD GLU E 270 " pdb=" OE1 GLU E 270 " ideal model delta sinusoidal sigma weight residual 0.00 -83.02 83.02 1 3.00e+01 1.11e-03 9.37e+00 ... (remaining 8110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 751 0.032 - 0.064: 644 0.064 - 0.097: 378 0.097 - 0.129: 159 0.129 - 0.161: 35 Chirality restraints: 1967 Sorted by residual: chirality pdb=" CA ASN C 273 " pdb=" N ASN C 273 " pdb=" C ASN C 273 " pdb=" CB ASN C 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ASN E 273 " pdb=" N ASN E 273 " pdb=" C ASN E 273 " pdb=" CB ASN E 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ASN F 273 " pdb=" N ASN F 273 " pdb=" C ASN F 273 " pdb=" CB ASN F 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1964 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 81 " -0.019 2.00e-02 2.50e+03 1.21e-02 2.94e+00 pdb=" CG TYR A 81 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 81 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 81 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 81 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 81 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 81 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 81 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 81 " -0.019 2.00e-02 2.50e+03 1.21e-02 2.93e+00 pdb=" CG TYR C 81 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 81 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 81 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 81 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 81 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 81 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 81 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 273 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" CG ASN A 273 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 273 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 273 " 0.010 2.00e-02 2.50e+03 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 604 2.69 - 3.24: 13166 3.24 - 3.80: 22991 3.80 - 4.35: 25703 4.35 - 4.90: 42627 Nonbonded interactions: 105091 Sorted by model distance: nonbonded pdb=" OE1 GLU C 257 " pdb=" NH1 ARG D 221 " model vdw 2.141 2.520 nonbonded pdb=" OE1 GLU E 257 " pdb=" NH1 ARG F 221 " model vdw 2.145 2.520 nonbonded pdb=" OE1 GLU B 257 " pdb=" NH1 ARG C 221 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLU D 257 " pdb=" NH1 ARG E 221 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLU A 257 " pdb=" NH1 ARG B 221 " model vdw 2.151 2.520 ... (remaining 105086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8008 2.51 5 N 2247 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.020 Extract box with map and model: 4.590 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.120 Process input model: 36.320 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.016 0.078 13111 Z= 1.025 Angle : 0.943 7.606 17815 Z= 0.523 Chirality : 0.059 0.161 1967 Planarity : 0.006 0.041 2401 Dihedral : 14.023 83.055 4921 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.00 % 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: 1.90 (0.20), residues: 1624 helix: 1.71 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.07 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.546 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 1.4003 time to fit residues: 600.9167 Evaluate side-chains 256 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 253 GLN D 244 GLN E 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13111 Z= 0.183 Angle : 0.511 9.321 17815 Z= 0.265 Chirality : 0.033 0.118 1967 Planarity : 0.003 0.032 2401 Dihedral : 3.616 13.329 1764 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.85 (0.20), residues: 1624 helix: 3.15 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.72 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 299 time to evaluate : 1.551 Fit side-chains outliers start: 38 outliers final: 9 residues processed: 318 average time/residue: 1.0953 time to fit residues: 380.8295 Evaluate side-chains 293 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 284 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 8 average time/residue: 0.2614 time to fit residues: 4.9368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 117 optimal weight: 0.0870 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 13111 Z= 0.188 Angle : 0.463 5.272 17815 Z= 0.242 Chirality : 0.033 0.121 1967 Planarity : 0.003 0.031 2401 Dihedral : 3.373 12.324 1764 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.20), residues: 1624 helix: 3.72 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.11 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 295 time to evaluate : 1.626 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 315 average time/residue: 1.0291 time to fit residues: 357.2420 Evaluate side-chains 295 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 277 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 11 average time/residue: 0.4002 time to fit residues: 7.5226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN F 253 GLN G 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 13111 Z= 0.419 Angle : 0.605 6.037 17815 Z= 0.317 Chirality : 0.039 0.129 1967 Planarity : 0.005 0.034 2401 Dihedral : 3.720 14.557 1764 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.20), residues: 1624 helix: 3.34 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.15 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 1.790 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 296 average time/residue: 1.0589 time to fit residues: 344.4889 Evaluate side-chains 291 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 266 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.1519 time to fit residues: 4.6097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 253 GLN E 253 GLN F 253 GLN G 264 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13111 Z= 0.199 Angle : 0.476 5.295 17815 Z= 0.250 Chirality : 0.033 0.119 1967 Planarity : 0.004 0.032 2401 Dihedral : 3.400 13.036 1764 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.77 (0.20), residues: 1624 helix: 3.78 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.21 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 277 time to evaluate : 1.759 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 27 residues processed: 305 average time/residue: 1.0898 time to fit residues: 364.9578 Evaluate side-chains 296 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 16 residues processed: 11 average time/residue: 0.4604 time to fit residues: 8.2228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.0470 chunk 38 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 GLN G 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13111 Z= 0.173 Angle : 0.455 4.679 17815 Z= 0.237 Chirality : 0.032 0.123 1967 Planarity : 0.003 0.034 2401 Dihedral : 3.252 11.961 1764 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.09 (0.20), residues: 1624 helix: 4.03 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.28 (0.32), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 291 time to evaluate : 1.581 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 315 average time/residue: 1.0214 time to fit residues: 355.0529 Evaluate side-chains 302 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 281 time to evaluate : 1.619 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.3176 time to fit residues: 5.2797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 94 optimal weight: 0.0050 chunk 71 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13111 Z= 0.152 Angle : 0.446 6.376 17815 Z= 0.231 Chirality : 0.032 0.137 1967 Planarity : 0.003 0.035 2401 Dihedral : 3.161 13.884 1764 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.33 (0.20), residues: 1624 helix: 4.19 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.41 (0.33), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 294 time to evaluate : 1.627 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 313 average time/residue: 1.0294 time to fit residues: 355.1773 Evaluate side-chains 305 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 288 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.4508 time to fit residues: 4.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8545 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13111 Z= 0.167 Angle : 0.449 5.234 17815 Z= 0.233 Chirality : 0.032 0.140 1967 Planarity : 0.004 0.037 2401 Dihedral : 3.148 13.229 1764 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.35 (0.20), residues: 1624 helix: 4.20 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.44 (0.33), residues: 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 296 time to evaluate : 1.567 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 317 average time/residue: 1.0919 time to fit residues: 380.5638 Evaluate side-chains 307 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 291 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.8330 time to fit residues: 6.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8563 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13111 Z= 0.207 Angle : 0.486 6.526 17815 Z= 0.250 Chirality : 0.034 0.153 1967 Planarity : 0.004 0.039 2401 Dihedral : 3.234 12.999 1764 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.24 (0.20), residues: 1624 helix: 4.10 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.48 (0.32), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 291 time to evaluate : 1.557 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 309 average time/residue: 1.0129 time to fit residues: 345.5423 Evaluate side-chains 297 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 281 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.4653 time to fit residues: 4.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 0.0010 chunk 147 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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: 0.8548 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13111 Z= 0.171 Angle : 0.465 7.620 17815 Z= 0.240 Chirality : 0.033 0.162 1967 Planarity : 0.004 0.042 2401 Dihedral : 3.175 14.128 1764 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.35 (0.20), residues: 1624 helix: 4.18 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.51 (0.33), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 293 time to evaluate : 1.633 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 308 average time/residue: 1.0371 time to fit residues: 352.0397 Evaluate side-chains 303 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 289 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1693 time to fit residues: 2.5651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.084289 restraints weight = 20790.654| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.12 r_work: 0.3155 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 0.94 restraints_weight: 0.2500 r_work: 0.3131 rms_B_bonded: 1.01 restraints_weight: 0.1250 r_work: 0.3118 rms_B_bonded: 1.12 restraints_weight: 0.0625 r_work: 0.3104 rms_B_bonded: 1.27 restraints_weight: 0.0312 r_work: 0.3087 rms_B_bonded: 1.47 restraints_weight: 0.0156 r_work: 0.3069 rms_B_bonded: 1.71 restraints_weight: 0.0078 r_work: 0.3048 rms_B_bonded: 2.00 restraints_weight: 0.0039 r_work: 0.3025 rms_B_bonded: 2.35 restraints_weight: 0.0020 r_work: 0.2998 rms_B_bonded: 2.77 restraints_weight: 0.0010 r_work: 0.2968 rms_B_bonded: 3.26 restraints_weight: 0.0005 r_work: 0.2933 rms_B_bonded: 3.86 restraints_weight: 0.0002 r_work: 0.2893 rms_B_bonded: 4.57 restraints_weight: 0.0001 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 13111 Z= 0.262 Angle : 0.525 6.871 17815 Z= 0.270 Chirality : 0.035 0.142 1967 Planarity : 0.004 0.040 2401 Dihedral : 3.360 14.433 1764 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.03 (0.20), residues: 1624 helix: 3.92 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.48 (0.32), residues: 420 =============================================================================== Job complete usr+sys time: 5305.89 seconds wall clock time: 94 minutes 12.88 seconds (5652.88 seconds total)