Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 10:36:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/07_2023/7ytw_34094_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/07_2023/7ytw_34094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/07_2023/7ytw_34094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/07_2023/7ytw_34094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/07_2023/7ytw_34094_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/07_2023/7ytw_34094_updated.pdb" } resolution = 3.2 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= 0.034 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 5074 2.51 5 N 1238 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 7744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3857 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 33, 'TRANS': 473} Chain breaks: 2 Chain: "B" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3857 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 33, 'TRANS': 473} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'ASC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'ASC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.46, per 1000 atoms: 0.58 Number of scatterers: 7744 At special positions: 0 Unit cell: (87.74, 107.42, 76.26, 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 64 16.00 Na 4 11.00 O 1364 8.00 N 1238 7.00 C 5074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 136 " distance=2.03 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: 2.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 58.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 52 through 76 removed outlier: 4.630A pdb=" N GLY A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 83 through 104 Processing helix chain 'A' and resid 120 through 128 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 153 through 179 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 192 through 205 Proline residue: A 197 - end of helix removed outlier: 3.556A pdb=" N SER A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.317A pdb=" N SER A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.589A pdb=" N ALA A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 352 Processing helix chain 'A' and resid 360 through 380 Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.802A pdb=" N GLY A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 432 through 454 removed outlier: 4.054A pdb=" N ASN A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 484 Proline residue: A 479 - end of helix Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'B' and resid 52 through 76 removed outlier: 4.630A pdb=" N GLY B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 83 through 104 Processing helix chain 'B' and resid 120 through 128 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 153 through 179 Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 192 through 205 Proline residue: B 197 - end of helix removed outlier: 3.556A pdb=" N SER B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.317A pdb=" N SER B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 263 through 281 removed outlier: 3.589A pdb=" N ALA B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 352 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 398 removed outlier: 3.802A pdb=" N GLY B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 432 through 454 removed outlier: 4.054A pdb=" N ASN B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 484 Proline residue: B 479 - end of helix Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 513 through 521 394 hydrogen bonds defined for protein. 1182 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: 2.06 Time building geometry restraints manager: 3.22 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: 1816 1.33 - 1.45: 1622 1.45 - 1.57: 4398 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 7936 Sorted by residual: bond pdb=" C1 ASC A 703 " pdb=" O4 ASC A 703 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 ASC B 703 " pdb=" O4 ASC B 703 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" CG PRO A 197 " pdb=" CD PRO A 197 " ideal model delta sigma weight residual 1.503 1.369 0.134 3.40e-02 8.65e+02 1.55e+01 bond pdb=" CG PRO B 197 " pdb=" CD PRO B 197 " ideal model delta sigma weight residual 1.503 1.369 0.134 3.40e-02 8.65e+02 1.55e+01 bond pdb=" CG1 ILE A 93 " pdb=" CD1 ILE A 93 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.16e+00 ... (remaining 7931 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.06: 182 104.06 - 111.64: 3476 111.64 - 119.22: 3048 119.22 - 126.79: 3996 126.79 - 134.37: 130 Bond angle restraints: 10832 Sorted by residual: angle pdb=" CA PRO B 197 " pdb=" N PRO B 197 " pdb=" CD PRO B 197 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" CA PRO A 197 " pdb=" N PRO A 197 " pdb=" CD PRO A 197 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" N PRO A 197 " pdb=" CD PRO A 197 " pdb=" CG PRO A 197 " ideal model delta sigma weight residual 103.20 96.54 6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" N PRO B 197 " pdb=" CD PRO B 197 " pdb=" CG PRO B 197 " ideal model delta sigma weight residual 103.20 96.54 6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" CA THR A 196 " pdb=" CB THR A 196 " pdb=" CG2 THR A 196 " ideal model delta sigma weight residual 110.50 117.87 -7.37 1.70e+00 3.46e-01 1.88e+01 ... (remaining 10827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 4042 15.14 - 30.27: 480 30.27 - 45.41: 86 45.41 - 60.55: 10 60.55 - 75.69: 2 Dihedral angle restraints: 4620 sinusoidal: 1754 harmonic: 2866 Sorted by residual: dihedral pdb=" CA LEU B 201 " pdb=" C LEU B 201 " pdb=" N ILE B 202 " pdb=" CA ILE B 202 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LEU A 201 " pdb=" C LEU A 201 " pdb=" N ILE A 202 " pdb=" CA ILE A 202 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N GLY A 511 " pdb=" CA GLY A 511 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1058 0.079 - 0.157: 196 0.157 - 0.236: 14 0.236 - 0.315: 6 0.315 - 0.394: 8 Chirality restraints: 1282 Sorted by residual: chirality pdb=" C5 ASC A 703 " pdb=" C4 ASC A 703 " pdb=" C6 ASC A 703 " pdb=" O5 ASC A 703 " both_signs ideal model delta sigma weight residual False 2.26 2.65 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C5 ASC B 703 " pdb=" C4 ASC B 703 " pdb=" C6 ASC B 703 " pdb=" O5 ASC B 703 " both_signs ideal model delta sigma weight residual False 2.26 2.65 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB ILE B 569 " pdb=" CA ILE B 569 " pdb=" CG1 ILE B 569 " pdb=" CG2 ILE B 569 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1279 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B 288 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 288 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 262 " -0.019 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE A 262 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 262 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 262 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 262 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 262 " 0.000 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1450 2.76 - 3.30: 7554 3.30 - 3.83: 13718 3.83 - 4.37: 16566 4.37 - 4.90: 28239 Nonbonded interactions: 67527 Sorted by model distance: nonbonded pdb="NA NA B 701 " pdb=" O1 ASC B 703 " model vdw 2.230 2.470 nonbonded pdb="NA NA A 701 " pdb=" O1 ASC A 703 " model vdw 2.230 2.470 nonbonded pdb=" O SER A 117 " pdb=" O3 ASC A 703 " model vdw 2.273 2.440 nonbonded pdb=" O SER B 117 " pdb=" O3 ASC B 703 " model vdw 2.273 2.440 nonbonded pdb=" O CYS A 275 " pdb=" OG1 THR A 279 " model vdw 2.303 2.440 ... (remaining 67522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.050 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: 12.490 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.950 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.009 0.134 7936 Z= 0.567 Angle : 1.112 9.372 10832 Z= 0.586 Chirality : 0.068 0.394 1282 Planarity : 0.010 0.087 1346 Dihedral : 12.981 75.687 2786 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1002 helix: -1.97 (0.16), residues: 656 sheet: -4.36 (0.58), residues: 20 loop : -1.55 (0.36), residues: 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.809 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1685 time to fit residues: 23.8430 Evaluate side-chains 82 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7936 Z= 0.236 Angle : 0.639 7.660 10832 Z= 0.332 Chirality : 0.044 0.149 1282 Planarity : 0.007 0.061 1346 Dihedral : 5.359 21.170 1080 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.26), residues: 1002 helix: -0.54 (0.19), residues: 662 sheet: -4.27 (0.59), residues: 20 loop : -1.40 (0.37), residues: 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.869 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.1544 time to fit residues: 23.0041 Evaluate side-chains 100 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0853 time to fit residues: 2.0841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 0.0170 chunk 61 optimal weight: 0.0000 chunk 25 optimal weight: 0.0170 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 overall best weight: 0.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7936 Z= 0.177 Angle : 0.571 7.756 10832 Z= 0.295 Chirality : 0.042 0.171 1282 Planarity : 0.006 0.052 1346 Dihedral : 4.869 18.791 1080 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -0.54 (0.27), residues: 1002 helix: 0.37 (0.20), residues: 650 sheet: -4.26 (0.57), residues: 20 loop : -1.45 (0.36), residues: 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.696 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 100 average time/residue: 0.1493 time to fit residues: 22.6535 Evaluate side-chains 90 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0754 time to fit residues: 1.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.0050 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.0040 chunk 54 optimal weight: 0.5980 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7936 Z= 0.195 Angle : 0.583 7.693 10832 Z= 0.296 Chirality : 0.043 0.176 1282 Planarity : 0.006 0.050 1346 Dihedral : 4.724 18.699 1080 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 1002 helix: 0.69 (0.20), residues: 650 sheet: -4.13 (0.61), residues: 20 loop : -1.33 (0.36), residues: 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.268 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.1612 time to fit residues: 22.2016 Evaluate side-chains 88 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0842 time to fit residues: 2.0707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 7936 Z= 0.493 Angle : 0.770 8.218 10832 Z= 0.393 Chirality : 0.051 0.201 1282 Planarity : 0.006 0.051 1346 Dihedral : 5.367 21.045 1080 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.90 % 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: -0.99 (0.26), residues: 1002 helix: 0.01 (0.19), residues: 642 sheet: -4.35 (0.66), residues: 20 loop : -1.56 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.855 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 0.1297 time to fit residues: 22.8008 Evaluate side-chains 98 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0895 time to fit residues: 2.4219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 7936 Z= 0.226 Angle : 0.629 12.258 10832 Z= 0.321 Chirality : 0.044 0.188 1282 Planarity : 0.006 0.048 1346 Dihedral : 4.960 20.220 1080 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: -0.40 (0.27), residues: 1002 helix: 0.47 (0.20), residues: 648 sheet: -4.26 (0.66), residues: 20 loop : -1.36 (0.36), residues: 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.799 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 0.1294 time to fit residues: 19.4467 Evaluate side-chains 90 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0759 time to fit residues: 1.4587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7936 Z= 0.264 Angle : 0.619 6.785 10832 Z= 0.319 Chirality : 0.045 0.174 1282 Planarity : 0.006 0.049 1346 Dihedral : 4.877 19.989 1080 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 1002 helix: 0.57 (0.20), residues: 648 sheet: -4.11 (0.68), residues: 20 loop : -1.27 (0.37), residues: 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.833 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 0.1310 time to fit residues: 20.2284 Evaluate side-chains 92 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0704 time to fit residues: 1.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.0000 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7936 Z= 0.280 Angle : 0.651 12.661 10832 Z= 0.330 Chirality : 0.045 0.175 1282 Planarity : 0.006 0.050 1346 Dihedral : 4.871 19.988 1080 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.24 % 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: -0.23 (0.27), residues: 1002 helix: 0.61 (0.20), residues: 646 sheet: -4.09 (0.71), residues: 20 loop : -1.30 (0.36), residues: 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.864 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 94 average time/residue: 0.1335 time to fit residues: 20.0110 Evaluate side-chains 92 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0781 time to fit residues: 1.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7936 Z= 0.300 Angle : 0.659 11.145 10832 Z= 0.335 Chirality : 0.046 0.186 1282 Planarity : 0.006 0.050 1346 Dihedral : 4.913 20.154 1080 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.27), residues: 1002 helix: 0.54 (0.20), residues: 646 sheet: -4.07 (0.71), residues: 20 loop : -1.30 (0.36), residues: 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.788 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1337 time to fit residues: 20.6398 Evaluate side-chains 96 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.0030 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7936 Z= 0.252 Angle : 0.630 11.084 10832 Z= 0.321 Chirality : 0.045 0.182 1282 Planarity : 0.006 0.050 1346 Dihedral : 4.822 19.795 1080 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.24 % 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: -0.11 (0.27), residues: 1002 helix: 0.72 (0.20), residues: 646 sheet: -4.11 (0.71), residues: 20 loop : -1.28 (0.37), residues: 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.775 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.1266 time to fit residues: 19.5227 Evaluate side-chains 90 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152384 restraints weight = 7308.025| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.28 r_work: 0.3733 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7936 Z= 0.225 Angle : 0.609 10.891 10832 Z= 0.309 Chirality : 0.044 0.174 1282 Planarity : 0.006 0.050 1346 Dihedral : 4.698 19.480 1080 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.24 % 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: 0.04 (0.27), residues: 1002 helix: 0.85 (0.20), residues: 646 sheet: -4.14 (0.69), residues: 20 loop : -1.23 (0.37), residues: 336 =============================================================================== Job complete usr+sys time: 1845.74 seconds wall clock time: 34 minutes 11.03 seconds (2051.03 seconds total)