Starting phenix.real_space_refine on Fri Nov 15 12:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ost_17164/11_2024/8ost_17164.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ost_17164/11_2024/8ost_17164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ost_17164/11_2024/8ost_17164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ost_17164/11_2024/8ost_17164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ost_17164/11_2024/8ost_17164.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ost_17164/11_2024/8ost_17164.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 S 26 5.16 5 C 2856 2.51 5 N 847 2.21 5 O 1097 1.98 5 H 4058 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8955 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 6193 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 21, 'TRANS': 368} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 604 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 2156 Classifications: {'RNA': 69} Modifications used: {'3*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 25} Link IDs: {'rna2p': 10, 'rna3p': 58} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6242 SG CYS B 139 46.190 33.375 93.580 1.00 95.55 S ATOM 6287 SG CYS B 142 48.791 31.460 95.469 1.00 97.85 S ATOM 6409 SG CYS B 152 49.806 33.602 92.464 1.00 96.98 S ATOM 6549 SG CYS B 161 42.049 17.731 99.911 1.00127.76 S ATOM 6597 SG CYS B 164 44.047 15.621 101.441 1.00131.34 S ATOM 6737 SG CYS B 174 40.227 14.399 101.994 1.00133.57 S Time building chain proxies: 5.59, per 1000 atoms: 0.62 Number of scatterers: 8955 At special positions: 0 Unit cell: (74.7, 74.7, 133.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 26 16.00 P 69 15.00 O 1097 8.00 N 847 7.00 C 2856 6.00 H 4058 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 498.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 147 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 139 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 152 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 142 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 164 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 161 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 174 " Number of angles added : 3 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 46.5% alpha, 2.5% beta 3 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.332A pdb=" N GLN A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'A' and resid 325 through 343 removed outlier: 3.722A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.575A pdb=" N THR A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 424 through 439 removed outlier: 3.773A pdb=" N ILE A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 490 removed outlier: 3.778A pdb=" N LEU A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.868A pdb=" N LEU A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 689 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'B' and resid 170 through 174 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA2, first strand: chain 'A' and resid 446 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.547A pdb=" N ILE A 651 " --> pdb=" O GLU A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 135 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 7 hydrogen bonds 14 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4040 1.02 - 1.22: 18 1.22 - 1.41: 2099 1.41 - 1.61: 3014 1.61 - 1.81: 33 Bond restraints: 9204 Sorted by residual: bond pdb=" NE2 GLN A 532 " pdb="HE22 GLN A 532 " ideal model delta sigma weight residual 0.860 0.821 0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CG PRO A 710 " pdb=" CD PRO A 710 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.67e+00 bond pdb=" O4' G C 20 " pdb=" C1' G C 20 " ideal model delta sigma weight residual 1.412 1.395 0.017 1.50e-02 4.44e+03 1.34e+00 bond pdb=" C3' G C 20 " pdb=" C2' G C 20 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.50e-02 4.44e+03 1.33e+00 bond pdb=" CB PRO A 710 " pdb=" CG PRO A 710 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.16e+00 ... (remaining 9199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 16101 1.50 - 3.00: 451 3.00 - 4.50: 40 4.50 - 5.99: 4 5.99 - 7.49: 3 Bond angle restraints: 16599 Sorted by residual: angle pdb=" C3' U C 61 " pdb=" C2' U C 61 " pdb=" C1' U C 61 " ideal model delta sigma weight residual 101.50 104.37 -2.87 1.00e+00 1.00e+00 8.22e+00 angle pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " ideal model delta sigma weight residual 102.60 105.43 -2.83 1.00e+00 1.00e+00 7.98e+00 angle pdb=" O3' A C 19 " pdb=" C3' A C 19 " pdb=" C2' A C 19 " ideal model delta sigma weight residual 113.70 117.89 -4.19 1.50e+00 4.44e-01 7.79e+00 angle pdb=" CA PRO A 710 " pdb=" N PRO A 710 " pdb=" CD PRO A 710 " ideal model delta sigma weight residual 112.00 108.12 3.88 1.40e+00 5.10e-01 7.69e+00 angle pdb=" C4' U C 61 " pdb=" C3' U C 61 " pdb=" C2' U C 61 " ideal model delta sigma weight residual 102.60 105.34 -2.74 1.00e+00 1.00e+00 7.51e+00 ... (remaining 16594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 3980 28.38 - 56.76: 324 56.76 - 85.14: 118 85.14 - 113.52: 17 113.52 - 141.90: 2 Dihedral angle restraints: 4441 sinusoidal: 2957 harmonic: 1484 Sorted by residual: dihedral pdb=" O4' G C 20 " pdb=" C2' G C 20 " pdb=" C1' G C 20 " pdb=" C3' G C 20 " ideal model delta sinusoidal sigma weight residual 25.00 -18.72 43.72 1 8.00e+00 1.56e-02 4.16e+01 dihedral pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " pdb=" C1' G C 20 " ideal model delta sinusoidal sigma weight residual 36.00 0.06 35.94 1 8.00e+00 1.56e-02 2.86e+01 dihedral pdb=" C4' G C 20 " pdb=" O4' G C 20 " pdb=" C1' G C 20 " pdb=" C2' G C 20 " ideal model delta sinusoidal sigma weight residual 3.00 -31.89 34.89 1 8.00e+00 1.56e-02 2.70e+01 ... (remaining 4438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 716 0.041 - 0.083: 116 0.083 - 0.124: 43 0.124 - 0.165: 4 0.165 - 0.206: 1 Chirality restraints: 880 Sorted by residual: chirality pdb=" C3' A C 19 " pdb=" C4' A C 19 " pdb=" O3' A C 19 " pdb=" C2' A C 19 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1' U C 14 " pdb=" O4' U C 14 " pdb=" C2' U C 14 " pdb=" N1 U C 14 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" C1' G C 15 " pdb=" O4' G C 15 " pdb=" C2' G C 15 " pdb=" N9 G C 15 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 877 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 532 " -0.062 2.00e-02 2.50e+03 7.96e-02 9.50e+01 pdb=" CD GLN A 532 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN A 532 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 532 " 0.126 2.00e-02 2.50e+03 pdb="HE21 GLN A 532 " 0.012 2.00e-02 2.50e+03 pdb="HE22 GLN A 532 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 414 " 0.036 2.00e-02 2.50e+03 6.09e-02 5.57e+01 pdb=" CG ASN A 414 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 414 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 414 " 0.103 2.00e-02 2.50e+03 pdb="HD21 ASN A 414 " 0.007 2.00e-02 2.50e+03 pdb="HD22 ASN A 414 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 709 " 0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 710 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 710 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 710 " 0.061 5.00e-02 4.00e+02 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 57 2.06 - 2.69: 12485 2.69 - 3.33: 24556 3.33 - 3.96: 31326 3.96 - 4.60: 46429 Nonbonded interactions: 114853 Sorted by model distance: nonbonded pdb=" HE1 HIS B 147 " pdb="ZN ZN B 301 " model vdw 1.422 1.408 nonbonded pdb="HD22 ASN A 424 " pdb=" OD2 ASP A 427 " model vdw 1.598 2.450 nonbonded pdb="HO2' A C 35 " pdb=" O4' U C 36 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASP A 675 " pdb=" HG SER A 678 " model vdw 1.804 2.450 nonbonded pdb=" O MET A 525 " pdb=" HH TYR A 640 " model vdw 1.817 2.450 ... (remaining 114848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.150 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.570 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 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 : 0.002 0.054 5146 Z= 0.145 Angle : 0.515 6.337 7305 Z= 0.290 Chirality : 0.037 0.206 880 Planarity : 0.006 0.113 671 Dihedral : 22.671 121.299 2369 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.27 % Allowed : 18.40 % Favored : 81.33 % 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: 0.21 (0.40), residues: 422 helix: 1.96 (0.41), residues: 168 sheet: -1.89 (0.87), residues: 34 loop : -0.99 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 570 HIS 0.001 0.000 HIS A 351 PHE 0.004 0.001 PHE A 700 TYR 0.005 0.001 TYR A 299 ARG 0.003 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.6349 (mptt) cc_final: 0.5411 (ttpt) REVERT: A 423 MET cc_start: 0.2818 (mmt) cc_final: 0.1685 (mpp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.4559 time to fit residues: 44.7601 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5146 Z= 0.191 Angle : 0.539 4.742 7305 Z= 0.288 Chirality : 0.036 0.194 880 Planarity : 0.005 0.065 671 Dihedral : 23.739 106.809 1526 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 19.73 % Favored : 79.73 % 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: 0.47 (0.41), residues: 422 helix: 2.09 (0.39), residues: 178 sheet: -1.46 (0.93), residues: 34 loop : -0.99 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 666 HIS 0.011 0.002 HIS B 169 PHE 0.020 0.001 PHE A 493 TYR 0.012 0.002 TYR A 640 ARG 0.005 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6639 (ptm-80) cc_final: 0.6328 (ptm-80) REVERT: A 364 LYS cc_start: 0.6426 (mptt) cc_final: 0.5492 (tttm) REVERT: A 406 PHE cc_start: 0.6799 (m-10) cc_final: 0.6539 (m-80) REVERT: A 423 MET cc_start: 0.2822 (mmt) cc_final: 0.1954 (mpp) REVERT: A 681 ARG cc_start: 0.6206 (tmt170) cc_final: 0.5981 (tmt170) outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.4536 time to fit residues: 33.7127 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 686 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5146 Z= 0.195 Angle : 0.506 6.367 7305 Z= 0.270 Chirality : 0.035 0.162 880 Planarity : 0.004 0.054 671 Dihedral : 23.565 106.853 1526 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.33 % Allowed : 19.20 % Favored : 79.47 % 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: 0.39 (0.40), residues: 422 helix: 2.06 (0.39), residues: 178 sheet: -2.40 (0.95), residues: 28 loop : -0.93 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 503 HIS 0.007 0.002 HIS A 328 PHE 0.020 0.002 PHE A 493 TYR 0.014 0.002 TYR A 399 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6517 (ptm-80) cc_final: 0.6206 (ptm-80) REVERT: A 423 MET cc_start: 0.2556 (mmt) cc_final: 0.1694 (mpp) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.4057 time to fit residues: 29.9448 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5146 Z= 0.216 Angle : 0.506 4.320 7305 Z= 0.271 Chirality : 0.035 0.141 880 Planarity : 0.004 0.054 671 Dihedral : 23.452 107.636 1526 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 21.60 % Favored : 76.27 % 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: 0.19 (0.40), residues: 422 helix: 1.92 (0.39), residues: 177 sheet: -2.64 (0.89), residues: 29 loop : -1.04 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 503 HIS 0.008 0.002 HIS A 328 PHE 0.015 0.002 PHE A 644 TYR 0.013 0.002 TYR A 640 ARG 0.003 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6593 (ptm-80) cc_final: 0.6367 (ptm-80) REVERT: A 412 ASP cc_start: 0.5652 (OUTLIER) cc_final: 0.3632 (m-30) REVERT: A 423 MET cc_start: 0.2639 (mmt) cc_final: 0.1384 (mpp) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.3699 time to fit residues: 26.9546 Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 HIS ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5146 Z= 0.208 Angle : 0.497 4.527 7305 Z= 0.265 Chirality : 0.035 0.157 880 Planarity : 0.004 0.050 671 Dihedral : 23.402 107.647 1526 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.40 % Allowed : 21.33 % Favored : 76.27 % 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: 0.26 (0.40), residues: 422 helix: 1.97 (0.39), residues: 177 sheet: -2.57 (0.90), residues: 29 loop : -0.98 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 PHE 0.017 0.002 PHE A 644 TYR 0.010 0.002 TYR A 693 ARG 0.001 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7881 (m-30) cc_final: 0.7671 (t0) REVERT: A 423 MET cc_start: 0.2566 (mmt) cc_final: 0.1310 (mpp) REVERT: A 644 PHE cc_start: 0.3465 (OUTLIER) cc_final: 0.2458 (p90) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.3555 time to fit residues: 25.6546 Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 644 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5146 Z= 0.191 Angle : 0.495 5.017 7305 Z= 0.262 Chirality : 0.035 0.145 880 Planarity : 0.004 0.043 671 Dihedral : 23.338 107.985 1526 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.40 % Allowed : 21.87 % Favored : 75.73 % 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 (0.40), residues: 422 helix: 1.82 (0.38), residues: 178 sheet: -2.49 (0.94), residues: 29 loop : -0.89 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.006 0.001 HIS A 328 PHE 0.013 0.001 PHE A 644 TYR 0.011 0.002 TYR A 640 ARG 0.003 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7876 (m-30) cc_final: 0.7673 (t0) REVERT: A 412 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.3643 (m-30) REVERT: A 423 MET cc_start: 0.2517 (mmt) cc_final: 0.1297 (mpp) REVERT: A 563 VAL cc_start: 0.7076 (t) cc_final: 0.5660 (m) REVERT: A 644 PHE cc_start: 0.3598 (OUTLIER) cc_final: 0.3016 (p90) REVERT: A 706 TYR cc_start: 0.6588 (t80) cc_final: 0.6157 (t80) REVERT: B 151 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5251 (mp0) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.3810 time to fit residues: 24.7689 Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5146 Z= 0.137 Angle : 0.469 8.462 7305 Z= 0.248 Chirality : 0.034 0.145 880 Planarity : 0.004 0.037 671 Dihedral : 23.246 107.322 1526 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.33 % Allowed : 21.60 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.41), residues: 422 helix: 2.01 (0.39), residues: 178 sheet: -2.27 (0.97), residues: 29 loop : -0.82 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS A 328 PHE 0.009 0.001 PHE A 644 TYR 0.008 0.001 TYR A 693 ARG 0.004 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2411 (mmt) cc_final: 0.1155 (mpp) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.3896 time to fit residues: 22.1369 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5146 Z= 0.147 Angle : 0.463 5.175 7305 Z= 0.244 Chirality : 0.034 0.145 880 Planarity : 0.004 0.038 671 Dihedral : 23.148 107.467 1526 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.87 % Allowed : 20.27 % Favored : 77.87 % 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: 0.56 (0.41), residues: 422 helix: 2.00 (0.39), residues: 179 sheet: -2.58 (1.03), residues: 24 loop : -0.66 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A 644 TYR 0.008 0.001 TYR A 693 ARG 0.004 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.6526 (mptt) cc_final: 0.5582 (tttm) REVERT: A 423 MET cc_start: 0.2357 (mmt) cc_final: 0.1085 (mpp) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.3987 time to fit residues: 23.6834 Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5146 Z= 0.217 Angle : 0.494 4.984 7305 Z= 0.265 Chirality : 0.035 0.151 880 Planarity : 0.004 0.037 671 Dihedral : 23.168 108.708 1526 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.13 % Allowed : 20.27 % Favored : 77.60 % 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: 0.21 (0.40), residues: 422 helix: 1.75 (0.38), residues: 178 sheet: -2.27 (0.97), residues: 29 loop : -0.90 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 PHE 0.019 0.001 PHE A 644 TYR 0.011 0.002 TYR A 640 ARG 0.005 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.3128 (m-30) REVERT: A 423 MET cc_start: 0.2413 (mmt) cc_final: 0.1146 (mpp) REVERT: A 563 VAL cc_start: 0.6895 (t) cc_final: 0.6106 (t) REVERT: A 706 TYR cc_start: 0.6614 (t80) cc_final: 0.6236 (t80) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.3979 time to fit residues: 25.0297 Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5146 Z= 0.201 Angle : 0.510 10.075 7305 Z= 0.273 Chirality : 0.035 0.158 880 Planarity : 0.004 0.038 671 Dihedral : 23.160 107.971 1526 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.13 % Allowed : 20.53 % Favored : 77.33 % 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 (0.40), residues: 422 helix: 1.74 (0.38), residues: 178 sheet: -2.15 (0.99), residues: 29 loop : -0.89 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.016 0.001 PHE A 522 TYR 0.010 0.002 TYR A 399 ARG 0.004 0.001 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.5551 (OUTLIER) cc_final: 0.3006 (m-30) REVERT: A 423 MET cc_start: 0.2384 (mmt) cc_final: 0.1125 (mpp) REVERT: A 706 TYR cc_start: 0.6640 (t80) cc_final: 0.6284 (t80) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.3823 time to fit residues: 23.8732 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** 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 = 0.4842 r_free = 0.4842 target = 0.249206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.198676 restraints weight = 18441.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.202804 restraints weight = 12636.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.203359 restraints weight = 10106.335| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5146 Z= 0.192 Angle : 0.504 10.014 7305 Z= 0.270 Chirality : 0.035 0.199 880 Planarity : 0.004 0.038 671 Dihedral : 23.149 107.837 1526 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.13 % Allowed : 21.07 % Favored : 76.80 % 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: 0.20 (0.40), residues: 422 helix: 1.76 (0.38), residues: 179 sheet: -2.16 (0.99), residues: 29 loop : -0.95 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.016 0.001 PHE A 522 TYR 0.010 0.001 TYR A 399 ARG 0.003 0.000 ARG A 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.79 seconds wall clock time: 59 minutes 6.56 seconds (3546.56 seconds total)