Starting phenix.real_space_refine on Thu Sep 26 07:58:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/09_2024/7p0z_13153.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/09_2024/7p0z_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_13153/09_2024/7p0z_13153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/09_2024/7p0z_13153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/09_2024/7p0z_13153.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0z_13153/09_2024/7p0z_13153.cif" } resolution = 2.43 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= 0.246 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 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. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12873 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.59, per 1000 atoms: 0.36 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 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: 0.95 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: 3.52 Time building geometry restraints manager: 3.76 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: 0.00 - 1.52: 16178 1.52 - 3.04: 1317 3.04 - 4.56: 257 4.56 - 6.08: 56 6.08 - 7.61: 7 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 3.120 nonbonded pdb=" OE1 GLU E 257 " pdb=" NH1 ARG F 221 " model vdw 2.145 3.120 nonbonded pdb=" OE1 GLU B 257 " pdb=" NH1 ARG C 221 " model vdw 2.148 3.120 nonbonded pdb=" OE1 GLU D 257 " pdb=" NH1 ARG E 221 " model vdw 2.148 3.120 nonbonded pdb=" OE1 GLU A 257 " pdb=" NH1 ARG B 221 " model vdw 2.151 3.120 ... (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 Time spend for trying shortcut: 0.00 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 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 25.960 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 156 HIS 0.009 0.004 HIS A 223 PHE 0.027 0.004 PHE D 159 TYR 0.028 0.006 TYR F 81 ARG 0.012 0.002 ARG A 165 *********************** 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 : 1.481 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.7647 (ptt-90) cc_final: 0.7442 (ptp90) REVERT: F 133 LEU cc_start: 0.8963 (mm) cc_final: 0.8714 (mt) REVERT: F 201 LEU cc_start: 0.9089 (mt) cc_final: 0.8878 (mt) REVERT: G 68 GLN cc_start: 0.8396 (mt0) cc_final: 0.8180 (mt0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 1.4449 time to fit residues: 618.0151 Evaluate side-chains 256 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 244 GLN E 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13111 Z= 0.211 Angle : 0.539 8.595 17815 Z= 0.280 Chirality : 0.034 0.128 1967 Planarity : 0.004 0.036 2401 Dihedral : 3.684 13.532 1764 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.90 % Allowed : 13.24 % Favored : 83.85 % 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: 3.81 (0.20), residues: 1624 helix: 3.10 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.80 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 156 HIS 0.003 0.001 HIS G 223 PHE 0.016 0.002 PHE E 152 TYR 0.017 0.002 TYR E 59 ARG 0.003 0.001 ARG G 234 *********************** 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 339 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 300 time to evaluate : 1.578 Fit side-chains REVERT: B 11 GLN cc_start: 0.8221 (mt0) cc_final: 0.7999 (mt0) REVERT: E 257 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6853 (mt-10) REVERT: F 133 LEU cc_start: 0.8863 (mm) cc_final: 0.8636 (mt) REVERT: F 201 LEU cc_start: 0.9038 (mt) cc_final: 0.8823 (mt) outliers start: 39 outliers final: 12 residues processed: 313 average time/residue: 1.1430 time to fit residues: 390.7540 Evaluate side-chains 296 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.0050 chunk 121 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13111 Z= 0.211 Angle : 0.489 5.873 17815 Z= 0.255 Chirality : 0.033 0.131 1967 Planarity : 0.004 0.035 2401 Dihedral : 3.444 13.306 1764 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 3.57 % Allowed : 14.36 % Favored : 82.07 % 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: 4.60 (0.20), residues: 1624 helix: 3.64 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.18 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 156 HIS 0.004 0.001 HIS B 223 PHE 0.016 0.002 PHE G 152 TYR 0.018 0.002 TYR B 59 ARG 0.007 0.000 ARG D 67 *********************** 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 336 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 288 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLN cc_start: 0.8212 (mt0) cc_final: 0.7989 (mt0) REVERT: C 134 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8287 (mttt) REVERT: C 141 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: C 221 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7323 (ptp90) REVERT: C 257 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6651 (mt-10) REVERT: D 59 TYR cc_start: 0.8255 (m-80) cc_final: 0.8026 (m-80) REVERT: D 221 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7407 (ptp90) REVERT: E 25 MET cc_start: 0.8248 (mtp) cc_final: 0.7981 (mtm) REVERT: E 192 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8670 (ttpt) REVERT: F 133 LEU cc_start: 0.8846 (mm) cc_final: 0.8604 (mt) REVERT: F 141 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: F 201 LEU cc_start: 0.9050 (mt) cc_final: 0.8829 (mt) REVERT: G 133 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8799 (mt) REVERT: G 134 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8598 (mmtp) REVERT: G 193 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7509 (mp0) outliers start: 48 outliers final: 22 residues processed: 311 average time/residue: 1.0998 time to fit residues: 375.0380 Evaluate side-chains 299 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 276 LYS 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: 0.0030 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13111 Z= 0.345 Angle : 0.572 5.794 17815 Z= 0.298 Chirality : 0.037 0.132 1967 Planarity : 0.005 0.037 2401 Dihedral : 3.625 13.816 1764 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.91 % Allowed : 15.85 % Favored : 79.24 % 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: 4.39 (0.20), residues: 1624 helix: 3.46 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.24 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 156 HIS 0.006 0.002 HIS G 223 PHE 0.020 0.003 PHE A 159 TYR 0.019 0.003 TYR B 59 ARG 0.003 0.000 ARG E 221 *********************** 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 339 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 273 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLN cc_start: 0.8240 (mt0) cc_final: 0.7989 (mt0) REVERT: C 134 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8268 (mttt) REVERT: C 141 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: D 221 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7417 (ptp90) REVERT: E 11 GLN cc_start: 0.8294 (mt0) cc_final: 0.8078 (mt0) REVERT: F 133 LEU cc_start: 0.8888 (mm) cc_final: 0.8627 (mt) REVERT: F 141 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: F 201 LEU cc_start: 0.9076 (mt) cc_final: 0.8861 (mt) REVERT: F 262 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: G 193 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7552 (mp0) outliers start: 66 outliers final: 28 residues processed: 308 average time/residue: 1.0878 time to fit residues: 367.2271 Evaluate side-chains 306 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 272 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN C 253 GLN G 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2250 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= 0.247 Angle : 0.511 5.246 17815 Z= 0.266 Chirality : 0.034 0.130 1967 Planarity : 0.004 0.034 2401 Dihedral : 3.460 13.104 1764 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 4.17 % Allowed : 17.78 % Favored : 78.05 % 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: 4.71 (0.20), residues: 1624 helix: 3.69 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 156 HIS 0.004 0.002 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.019 0.002 TYR A 59 ARG 0.004 0.000 ARG D 67 *********************** 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 343 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 287 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 134 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8318 (mttt) REVERT: C 141 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: D 59 TYR cc_start: 0.8267 (m-80) cc_final: 0.8022 (m-80) REVERT: E 11 GLN cc_start: 0.8248 (mt0) cc_final: 0.8033 (mt0) REVERT: F 141 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: F 201 LEU cc_start: 0.9059 (mt) cc_final: 0.8802 (mt) REVERT: G 193 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7524 (mp0) outliers start: 56 outliers final: 29 residues processed: 311 average time/residue: 1.1546 time to fit residues: 392.2232 Evaluate side-chains 299 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 266 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 0.0970 chunk 30 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN G 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13111 Z= 0.178 Angle : 0.470 5.404 17815 Z= 0.245 Chirality : 0.032 0.127 1967 Planarity : 0.004 0.032 2401 Dihedral : 3.265 12.557 1764 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.20 % Allowed : 19.27 % Favored : 77.53 % 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: 5.07 (0.20), residues: 1624 helix: 3.97 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.40 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.003 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.016 0.002 TYR A 59 ARG 0.005 0.000 ARG D 67 *********************** 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 329 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: C 134 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8303 (mttt) REVERT: C 141 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: F 141 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: F 201 LEU cc_start: 0.9042 (mt) cc_final: 0.8791 (mt) REVERT: G 133 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (mt) outliers start: 43 outliers final: 19 residues processed: 306 average time/residue: 1.0020 time to fit residues: 342.1158 Evaluate side-chains 294 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 270 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 133 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 71 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13111 Z= 0.165 Angle : 0.466 6.183 17815 Z= 0.241 Chirality : 0.032 0.129 1967 Planarity : 0.003 0.035 2401 Dihedral : 3.167 12.087 1764 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.75 % Allowed : 19.94 % Favored : 77.31 % 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: 5.22 (0.20), residues: 1624 helix: 4.09 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.44 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 156 HIS 0.003 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.017 0.002 TYR E 59 ARG 0.006 0.000 ARG D 67 *********************** 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 326 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 289 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: C 134 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8313 (mttt) REVERT: E 59 TYR cc_start: 0.8347 (m-80) cc_final: 0.7969 (m-80) REVERT: F 141 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: F 192 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8747 (ttpt) REVERT: F 201 LEU cc_start: 0.9037 (mt) cc_final: 0.8790 (mt) outliers start: 37 outliers final: 14 residues processed: 310 average time/residue: 1.0924 time to fit residues: 371.5273 Evaluate side-chains 294 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 278 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 VAL 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: 9.9990 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN F 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13111 Z= 0.358 Angle : 0.593 8.365 17815 Z= 0.307 Chirality : 0.038 0.128 1967 Planarity : 0.005 0.036 2401 Dihedral : 3.552 13.482 1764 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.65 % Allowed : 19.64 % Favored : 76.71 % 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: 4.62 (0.20), residues: 1624 helix: 3.61 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 156 HIS 0.007 0.003 HIS B 223 PHE 0.020 0.003 PHE A 159 TYR 0.023 0.003 TYR E 59 ARG 0.008 0.001 ARG D 67 *********************** 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 321 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 272 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 160 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8902 (t0) REVERT: C 134 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8304 (mttt) REVERT: C 226 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8184 (tt) REVERT: D 221 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7348 (ptp90) REVERT: F 141 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: F 201 LEU cc_start: 0.9077 (mt) cc_final: 0.8823 (mt) outliers start: 49 outliers final: 23 residues processed: 305 average time/residue: 1.0879 time to fit residues: 364.8116 Evaluate side-chains 294 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 0.0060 chunk 152 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN G 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13111 Z= 0.245 Angle : 0.529 6.076 17815 Z= 0.274 Chirality : 0.035 0.125 1967 Planarity : 0.004 0.037 2401 Dihedral : 3.414 13.028 1764 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.31 % Allowed : 21.43 % Favored : 76.26 % 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: 4.78 (0.20), residues: 1624 helix: 3.75 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.37 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 156 HIS 0.004 0.002 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.020 0.002 TYR E 59 ARG 0.016 0.000 ARG E 234 *********************** 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 303 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 160 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8841 (t0) REVERT: B 237 LYS cc_start: 0.7166 (tppt) cc_final: 0.6915 (tptt) REVERT: C 134 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8271 (mttt) REVERT: F 141 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: F 201 LEU cc_start: 0.9058 (mt) cc_final: 0.8787 (mt) outliers start: 31 outliers final: 21 residues processed: 289 average time/residue: 1.0392 time to fit residues: 330.9630 Evaluate side-chains 291 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 267 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 0.0050 chunk 147 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13111 Z= 0.217 Angle : 0.514 6.367 17815 Z= 0.266 Chirality : 0.034 0.126 1967 Planarity : 0.004 0.041 2401 Dihedral : 3.343 13.188 1764 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.01 % Allowed : 21.95 % Favored : 76.04 % 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: 4.92 (0.20), residues: 1624 helix: 3.86 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.39 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 156 HIS 0.004 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.017 0.002 TYR E 59 ARG 0.013 0.000 ARG E 234 ********************** 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 300 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 273 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 160 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8816 (t0) REVERT: C 134 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8282 (mttt) REVERT: D 59 TYR cc_start: 0.8303 (m-80) cc_final: 0.8069 (m-80) REVERT: F 141 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: F 201 LEU cc_start: 0.9050 (mt) cc_final: 0.8783 (mt) outliers start: 27 outliers final: 20 residues processed: 289 average time/residue: 1.0772 time to fit residues: 342.9166 Evaluate side-chains 290 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 267 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.0000 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN E 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086707 restraints weight = 20918.484| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.14 r_work: 0.3118 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13111 Z= 0.165 Angle : 0.483 6.268 17815 Z= 0.249 Chirality : 0.032 0.122 1967 Planarity : 0.004 0.043 2401 Dihedral : 3.163 13.684 1764 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.93 % Allowed : 21.95 % Favored : 76.12 % 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: 5.25 (0.20), residues: 1624 helix: 4.11 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 1.44 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 156 HIS 0.002 0.001 HIS B 223 PHE 0.017 0.002 PHE G 152 TYR 0.017 0.002 TYR E 59 ARG 0.012 0.000 ARG E 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.71 seconds wall clock time: 99 minutes 28.55 seconds (5968.55 seconds total)