Starting phenix.real_space_refine (version: dev) on Fri May 13 17:42:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/05_2022/6wu3_21904_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/05_2022/6wu3_21904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/05_2022/6wu3_21904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/05_2022/6wu3_21904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/05_2022/6wu3_21904_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/05_2022/6wu3_21904_neut.pdb" } resolution = 3.16 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= 0.000 sd= 1.000 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 None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 13610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6805 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6805 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.69, per 1000 atoms: 0.49 Number of scatterers: 13610 At special positions: 0 Unit cell: (90.789, 97.641, 76.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1128 8.00 N 1044 7.00 C 4450 6.00 H 6936 1.00 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: 12.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.596A pdb=" N LEU A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 79 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.795A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.521A pdb=" N ALA A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.796A pdb=" N ALA A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 4.021A pdb=" N TYR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.907A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 4.372A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.680A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 5.003A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 377 through 392 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 401 through 413 removed outlier: 3.754A pdb=" N SER A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 460 Processing helix chain 'C' and resid 19 through 38 removed outlier: 3.596A pdb=" N LEU C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 62 Processing helix chain 'C' and resid 65 through 79 Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.795A pdb=" N PHE C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.522A pdb=" N ALA C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.797A pdb=" N ALA C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 174 through 193 removed outlier: 4.022A pdb=" N TYR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.906A pdb=" N ALA C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 240 removed outlier: 4.372A pdb=" N PHE C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Proline residue: C 223 - end of helix Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 260 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 290 through 306 Processing helix chain 'C' and resid 310 through 318 Processing helix chain 'C' and resid 319 through 339 removed outlier: 3.679A pdb=" N LEU C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 5.003A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N MET C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 377 through 392 Proline residue: C 387 - end of helix Processing helix chain 'C' and resid 401 through 413 removed outlier: 3.754A pdb=" N SER C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 434 through 460 490 hydrogen bonds defined for protein. 1464 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: 4.52 Time building geometry restraints manager: 12.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6930 1.03 - 1.22: 6 1.22 - 1.42: 2757 1.42 - 1.61: 3977 1.61 - 1.80: 98 Bond restraints: 13768 Sorted by residual: bond pdb=" CG LEU A 197 " pdb=" CD1 LEU A 197 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG LEU C 197 " pdb=" CD1 LEU C 197 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG LEU A 301 " pdb=" CD2 LEU A 301 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU C 301 " pdb=" CD2 LEU C 301 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG1 ILE A 71 " pdb=" CD1 ILE A 71 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.31: 175 106.31 - 113.23: 16706 113.23 - 120.15: 4090 120.15 - 127.07: 3972 127.07 - 133.99: 81 Bond angle restraints: 25024 Sorted by residual: angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N VAL C 401 " pdb=" CA VAL C 401 " pdb=" C VAL C 401 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" CA VAL A 401 " pdb=" C VAL A 401 " pdb=" N LEU A 402 " ideal model delta sigma weight residual 118.65 115.98 2.67 1.07e+00 8.73e-01 6.23e+00 angle pdb=" CA VAL C 401 " pdb=" C VAL C 401 " pdb=" N LEU C 402 " ideal model delta sigma weight residual 118.65 116.02 2.63 1.07e+00 8.73e-01 6.04e+00 angle pdb=" CG LYS A 259 " pdb=" CD LYS A 259 " pdb=" CE LYS A 259 " ideal model delta sigma weight residual 111.30 116.30 -5.00 2.30e+00 1.89e-01 4.72e+00 ... (remaining 25019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4721 17.32 - 34.63: 523 34.63 - 51.95: 155 51.95 - 69.26: 38 69.26 - 86.58: 23 Dihedral angle restraints: 5460 sinusoidal: 2384 harmonic: 3076 Sorted by residual: dihedral pdb=" CA PHE C 83 " pdb=" C PHE C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE A 83 " pdb=" C PHE A 83 " pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE C 80 " pdb=" C PHE C 80 " pdb=" N GLY C 81 " pdb=" CA GLY C 81 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 575 0.024 - 0.048: 302 0.048 - 0.072: 209 0.072 - 0.097: 59 0.097 - 0.121: 13 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CA PRO C 418 " pdb=" N PRO C 418 " pdb=" C PRO C 418 " pdb=" CB PRO C 418 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA PRO A 418 " pdb=" N PRO A 418 " pdb=" C PRO A 418 " pdb=" CB PRO A 418 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE C 433 " pdb=" N ILE C 433 " pdb=" C ILE C 433 " pdb=" CB ILE C 433 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 422 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 421 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO C 422 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 422 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 422 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 159 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO C 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " -0.017 5.00e-02 4.00e+02 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 729 2.16 - 2.77: 27577 2.77 - 3.38: 39437 3.38 - 3.99: 50104 3.99 - 4.60: 80706 Nonbonded interactions: 198553 Sorted by model distance: nonbonded pdb=" O GLY A 184 " pdb=" HG SER A 188 " model vdw 1.555 1.850 nonbonded pdb=" O GLY C 184 " pdb=" HG SER C 188 " model vdw 1.575 1.850 nonbonded pdb=" O VAL C 57 " pdb=" HG1 THR C 61 " model vdw 1.607 1.850 nonbonded pdb=" O PRO C 387 " pdb=" HG1 THR C 391 " model vdw 1.611 1.850 nonbonded pdb=" O ILE C 267 " pdb=" HG1 THR C 271 " model vdw 1.614 1.850 ... (remaining 198548 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 'C' } 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4450 2.51 5 N 1044 2.21 5 O 1128 1.98 5 H 6936 0.53 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: 2.910 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: 0.230 Extract box with map and model: 12.890 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.120 Process input model: 47.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.008 0.042 6832 Z= 0.496 Angle : 0.603 4.997 9318 Z= 0.341 Chirality : 0.039 0.121 1158 Planarity : 0.004 0.037 1128 Dihedral : 15.887 84.129 2292 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 6.27 % 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: -3.62 (0.23), residues: 886 helix: -1.65 (0.16), residues: 696 sheet: None (None), residues: 0 loop : -4.72 (0.31), residues: 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 34 residues processed: 183 average time/residue: 0.3805 time to fit residues: 94.5369 Evaluate side-chains 162 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.120 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 2 residues processed: 34 average time/residue: 0.1631 time to fit residues: 11.2782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN C 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6832 Z= 0.191 Angle : 0.561 5.040 9318 Z= 0.295 Chirality : 0.035 0.128 1158 Planarity : 0.004 0.064 1128 Dihedral : 4.406 18.182 908 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 1.14 % 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: -1.43 (0.27), residues: 886 helix: -0.04 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -4.46 (0.36), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 146 average time/residue: 0.3062 time to fit residues: 64.6055 Evaluate side-chains 138 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.062 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1504 time to fit residues: 3.2288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 6832 Z= 0.387 Angle : 0.629 7.493 9318 Z= 0.330 Chirality : 0.037 0.141 1158 Planarity : 0.004 0.047 1128 Dihedral : 4.457 18.564 908 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 1.42 % 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: -0.79 (0.28), residues: 886 helix: 0.41 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -4.28 (0.37), residues: 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 156 average time/residue: 0.3505 time to fit residues: 75.3568 Evaluate side-chains 143 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.162 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.3813 time to fit residues: 4.8971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6832 Z= 0.249 Angle : 0.550 4.959 9318 Z= 0.288 Chirality : 0.035 0.137 1158 Planarity : 0.004 0.040 1128 Dihedral : 4.338 19.001 908 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.28 % 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: -0.24 (0.29), residues: 886 helix: 0.81 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.15 (0.37), residues: 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 149 average time/residue: 0.3421 time to fit residues: 72.8630 Evaluate side-chains 142 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.089 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1754 time to fit residues: 3.5220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 6832 Z= 0.382 Angle : 0.599 6.353 9318 Z= 0.315 Chirality : 0.037 0.146 1158 Planarity : 0.004 0.036 1128 Dihedral : 4.366 18.129 908 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 2.71 % 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: -0.13 (0.28), residues: 886 helix: 0.89 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.14 (0.36), residues: 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.3172 time to fit residues: 67.2797 Evaluate side-chains 148 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.062 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.1642 time to fit residues: 5.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 6832 Z= 0.250 Angle : 0.560 5.392 9318 Z= 0.293 Chirality : 0.035 0.163 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.317 20.927 908 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.85 % 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: 0.27 (0.29), residues: 886 helix: 1.17 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.01 (0.38), residues: 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 143 average time/residue: 0.3403 time to fit residues: 70.3500 Evaluate side-chains 136 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.075 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1605 time to fit residues: 2.4811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6832 Z= 0.211 Angle : 0.543 5.111 9318 Z= 0.280 Chirality : 0.035 0.174 1158 Planarity : 0.004 0.036 1128 Dihedral : 4.246 21.160 908 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.85 % 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: 0.54 (0.29), residues: 886 helix: 1.35 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -3.88 (0.38), residues: 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 143 average time/residue: 0.3289 time to fit residues: 66.3198 Evaluate side-chains 138 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.068 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1645 time to fit residues: 2.5652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6832 Z= 0.201 Angle : 0.537 4.875 9318 Z= 0.277 Chirality : 0.035 0.174 1158 Planarity : 0.003 0.036 1128 Dihedral : 4.184 22.065 908 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.71 % 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: 0.70 (0.30), residues: 886 helix: 1.47 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -3.84 (0.39), residues: 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 139 average time/residue: 0.3396 time to fit residues: 66.2888 Evaluate side-chains 134 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.156 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1646 time to fit residues: 2.6005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6832 Z= 0.180 Angle : 0.531 5.059 9318 Z= 0.272 Chirality : 0.034 0.183 1158 Planarity : 0.003 0.037 1128 Dihedral : 4.113 21.411 908 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.30), residues: 886 helix: 1.59 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -3.79 (0.39), residues: 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 141 average time/residue: 0.3232 time to fit residues: 64.6320 Evaluate side-chains 141 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.059 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1552 time to fit residues: 2.4924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6832 Z= 0.201 Angle : 0.532 4.874 9318 Z= 0.273 Chirality : 0.034 0.173 1158 Planarity : 0.004 0.038 1128 Dihedral : 4.075 20.638 908 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.71 % 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: 0.91 (0.30), residues: 886 helix: 1.61 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -3.73 (0.40), residues: 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 139 average time/residue: 0.3274 time to fit residues: 65.0510 Evaluate side-chains 138 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.977 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1618 time to fit residues: 2.4708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091601 restraints weight = 28285.658| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.22 r_work: 0.2871 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2839 rms_B_bonded: 2.09 restraints_weight: 0.1250 r_work: 0.2821 rms_B_bonded: 2.25 restraints_weight: 0.0625 r_work: 0.2802 rms_B_bonded: 2.48 restraints_weight: 0.0312 r_work: 0.2780 rms_B_bonded: 2.78 restraints_weight: 0.0156 r_work: 0.2756 rms_B_bonded: 3.16 restraints_weight: 0.0078 r_work: 0.2729 rms_B_bonded: 3.63 restraints_weight: 0.0039 r_work: 0.2698 rms_B_bonded: 4.21 restraints_weight: 0.0020 r_work: 0.2664 rms_B_bonded: 4.92 restraints_weight: 0.0010 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6832 Z= 0.220 Angle : 0.537 4.974 9318 Z= 0.277 Chirality : 0.035 0.180 1158 Planarity : 0.004 0.038 1128 Dihedral : 4.072 20.477 908 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.30), residues: 886 helix: 1.68 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -3.61 (0.40), residues: 182 =============================================================================== Job complete usr+sys time: 3323.91 seconds wall clock time: 59 minutes 22.55 seconds (3562.55 seconds total)