Starting phenix.real_space_refine on Tue Apr 29 21:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ost_17164/04_2025/8ost_17164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ost_17164/04_2025/8ost_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/cci-nas-00/data/ceres_data/8ost_17164/04_2025/8ost_17164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ost_17164/04_2025/8ost_17164.map" model { file = "/net/cci-nas-00/data/ceres_data/8ost_17164/04_2025/8ost_17164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ost_17164/04_2025/8ost_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 2.50 Conformation dependent library (CDL) restraints added in 508.8 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: 3.93 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: 2.71 Time building geometry restraints manager: 3.01 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: 3.390 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: 0.160 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 0.078 5153 Z= 0.108 Angle : 0.520 6.337 7308 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 Details of bonding type rmsd hydrogen bonds : bond 0.17730 ( 142) hydrogen bonds : angle 6.47354 ( 392) metal coordination : bond 0.02990 ( 7) metal coordination : angle 3.43786 ( 3) covalent geometry : bond 0.00224 ( 5146) covalent geometry : angle 0.51525 ( 7305) *********************** 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 : 0.563 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: 0.4252 time to fit residues: 41.4204 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 : 0.928 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4954 r_free = 0.4954 target = 0.261886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.210461 restraints weight = 19211.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.216787 restraints weight = 10534.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.221075 restraints weight = 6953.869| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5153 Z= 0.130 Angle : 0.549 5.239 7308 Z= 0.290 Chirality : 0.036 0.193 880 Planarity : 0.005 0.061 671 Dihedral : 23.719 106.504 1526 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 19.20 % Favored : 80.27 % 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: 0.45 (0.40), residues: 422 helix: 2.08 (0.39), residues: 178 sheet: -1.47 (0.93), residues: 34 loop : -1.00 (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 0.022 0.001 PHE A 493 TYR 0.012 0.002 TYR A 640 ARG 0.004 0.001 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 142) hydrogen bonds : angle 4.91479 ( 392) metal coordination : bond 0.02557 ( 7) metal coordination : angle 3.41115 ( 3) covalent geometry : bond 0.00280 ( 5146) covalent geometry : angle 0.54446 ( 7305) *********************** 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 : 0.590 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: A 291 ARG cc_start: 0.6500 (ptm-80) cc_final: 0.6208 (ptm-80) REVERT: A 364 LYS cc_start: 0.5776 (mptt) cc_final: 0.5336 (tttm) REVERT: A 423 MET cc_start: 0.2858 (mmt) cc_final: 0.2031 (mpp) outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.4460 time to fit residues: 33.1199 Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 16 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.256352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.201860 restraints weight = 19306.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.208311 restraints weight = 10992.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.212603 restraints weight = 7443.249| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5153 Z= 0.147 Angle : 0.518 5.700 7308 Z= 0.276 Chirality : 0.035 0.160 880 Planarity : 0.004 0.057 671 Dihedral : 23.581 107.134 1526 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.33 % Allowed : 19.47 % Favored : 79.20 % 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: 0.33 (0.40), residues: 422 helix: 1.99 (0.39), residues: 178 sheet: -2.43 (0.94), residues: 28 loop : -0.95 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 503 HIS 0.009 0.002 HIS A 328 PHE 0.011 0.002 PHE A 644 TYR 0.015 0.002 TYR A 399 ARG 0.003 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 142) hydrogen bonds : angle 4.79796 ( 392) metal coordination : bond 0.02471 ( 7) metal coordination : angle 3.11917 ( 3) covalent geometry : bond 0.00330 ( 5146) covalent geometry : angle 0.51461 ( 7305) *********************** 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 58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.629 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: 0.6305 (ptm-80) cc_final: 0.6039 (ptm-80) REVERT: A 423 MET cc_start: 0.2640 (mmt) cc_final: 0.1803 (mpp) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.3809 time to fit residues: 26.9566 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 : 0.621 ------------------------------------------------------------------------------- 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 48 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.253446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.198281 restraints weight = 18925.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.204579 restraints weight = 11040.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.208459 restraints weight = 7534.844| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5153 Z= 0.149 Angle : 0.516 4.351 7308 Z= 0.274 Chirality : 0.035 0.140 880 Planarity : 0.004 0.055 671 Dihedral : 23.468 107.613 1526 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.87 % Allowed : 21.33 % 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: 0.17 (0.40), residues: 422 helix: 1.90 (0.39), residues: 177 sheet: -2.67 (0.88), 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 0.006 0.001 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 142) hydrogen bonds : angle 4.58829 ( 392) metal coordination : bond 0.02507 ( 7) metal coordination : angle 2.72150 ( 3) covalent geometry : bond 0.00342 ( 5146) covalent geometry : angle 0.51325 ( 7305) *********************** 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 58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.4230 (m-30) REVERT: A 423 MET cc_start: 0.2677 (mmt) cc_final: 0.1421 (mpp) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.3706 time to fit residues: 26.3066 Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.253141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.197832 restraints weight = 19282.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.204208 restraints weight = 11320.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.208122 restraints weight = 7800.665| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5153 Z= 0.121 Angle : 0.489 4.451 7308 Z= 0.257 Chirality : 0.035 0.144 880 Planarity : 0.004 0.046 671 Dihedral : 23.379 107.303 1526 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 0.34 (0.40), residues: 422 helix: 1.99 (0.39), residues: 177 sheet: -2.46 (0.93), residues: 29 loop : -0.90 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 570 HIS 0.006 0.001 HIS A 328 PHE 0.015 0.001 PHE A 567 TYR 0.010 0.002 TYR A 399 ARG 0.003 0.001 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 142) hydrogen bonds : angle 4.37581 ( 392) metal coordination : bond 0.02510 ( 7) metal coordination : angle 2.59855 ( 3) covalent geometry : bond 0.00279 ( 5146) covalent geometry : angle 0.48640 ( 7305) *********************** 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 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2541 (mmt) cc_final: 0.1294 (mpp) REVERT: A 644 PHE cc_start: 0.4495 (OUTLIER) cc_final: 0.3481 (p90) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.3684 time to fit residues: 23.3600 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 : 0.562 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.249598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.198725 restraints weight = 18652.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.202691 restraints weight = 12765.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.202983 restraints weight = 9139.944| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5153 Z= 0.152 Angle : 0.521 5.265 7308 Z= 0.277 Chirality : 0.035 0.144 880 Planarity : 0.004 0.043 671 Dihedral : 23.355 108.615 1526 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.93 % Allowed : 20.80 % 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 (0.39), residues: 422 helix: 1.62 (0.38), residues: 179 sheet: -2.69 (1.01), residues: 24 loop : -0.81 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 PHE 0.017 0.001 PHE A 644 TYR 0.013 0.002 TYR A 640 ARG 0.003 0.001 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 142) hydrogen bonds : angle 4.52820 ( 392) metal coordination : bond 0.02498 ( 7) metal coordination : angle 2.39604 ( 3) covalent geometry : bond 0.00348 ( 5146) covalent geometry : angle 0.51934 ( 7305) *********************** 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 55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.4318 (m-30) REVERT: A 423 MET cc_start: 0.2575 (mmt) cc_final: 0.1349 (mpp) REVERT: A 563 VAL cc_start: 0.7244 (t) cc_final: 0.5954 (m) REVERT: A 644 PHE cc_start: 0.4938 (OUTLIER) cc_final: 0.4475 (p90) REVERT: A 706 TYR cc_start: 0.6904 (t80) cc_final: 0.6480 (t80) REVERT: B 151 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5950 (mp0) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.3798 time to fit residues: 25.3885 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- 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 = 0.4851 r_free = 0.4851 target = 0.250616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.201371 restraints weight = 19118.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.205860 restraints weight = 13658.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.206639 restraints weight = 10559.825| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5153 Z= 0.118 Angle : 0.490 8.229 7308 Z= 0.260 Chirality : 0.035 0.145 880 Planarity : 0.004 0.036 671 Dihedral : 23.301 108.002 1526 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.53 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: 0.31 (0.40), residues: 422 helix: 1.75 (0.38), residues: 179 sheet: -2.56 (1.04), residues: 24 loop : -0.78 (0.39), residues: 219 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 0.013 0.001 PHE A 644 TYR 0.009 0.001 TYR A 693 ARG 0.003 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 142) hydrogen bonds : angle 4.39974 ( 392) metal coordination : bond 0.02380 ( 7) metal coordination : angle 2.32605 ( 3) covalent geometry : bond 0.00267 ( 5146) covalent geometry : angle 0.48752 ( 7305) *********************** 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 51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2575 (mmt) cc_final: 0.1326 (mpp) REVERT: A 644 PHE cc_start: 0.4972 (OUTLIER) cc_final: 0.4622 (p90) REVERT: A 706 TYR cc_start: 0.6861 (t80) cc_final: 0.6479 (t80) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.3976 time to fit residues: 24.8973 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.247605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191729 restraints weight = 18760.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.197218 restraints weight = 11429.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.200683 restraints weight = 8153.912| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5153 Z= 0.162 Angle : 0.522 4.722 7308 Z= 0.279 Chirality : 0.036 0.153 880 Planarity : 0.004 0.037 671 Dihedral : 23.291 108.757 1526 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -0.03 (0.39), residues: 422 helix: 1.55 (0.38), residues: 178 sheet: -2.45 (0.93), residues: 29 loop : -1.02 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.009 0.001 HIS A 328 PHE 0.019 0.001 PHE A 644 TYR 0.013 0.002 TYR A 399 ARG 0.004 0.001 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 142) hydrogen bonds : angle 4.56820 ( 392) metal coordination : bond 0.02319 ( 7) metal coordination : angle 2.39390 ( 3) covalent geometry : bond 0.00379 ( 5146) covalent geometry : angle 0.51990 ( 7305) *********************** 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 56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2609 (mmt) cc_final: 0.1386 (mpp) REVERT: A 706 TYR cc_start: 0.6977 (t80) cc_final: 0.6562 (t80) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.4058 time to fit residues: 28.3107 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.248128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.197581 restraints weight = 18550.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.199471 restraints weight = 12593.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.200438 restraints weight = 9634.306| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5153 Z= 0.134 Angle : 0.504 5.259 7308 Z= 0.269 Chirality : 0.035 0.159 880 Planarity : 0.004 0.036 671 Dihedral : 23.250 108.015 1526 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -0.00 (0.40), residues: 422 helix: 1.55 (0.38), residues: 178 sheet: -2.31 (0.97), residues: 29 loop : -1.01 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.001 PHE A 644 TYR 0.011 0.002 TYR A 399 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 142) hydrogen bonds : angle 4.44899 ( 392) metal coordination : bond 0.02318 ( 7) metal coordination : angle 2.48925 ( 3) covalent geometry : bond 0.00311 ( 5146) covalent geometry : angle 0.50108 ( 7305) *********************** 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 : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.4235 (m-30) REVERT: A 423 MET cc_start: 0.2543 (mmt) cc_final: 0.1280 (mpp) REVERT: A 563 VAL cc_start: 0.7085 (t) cc_final: 0.6502 (t) REVERT: A 706 TYR cc_start: 0.6868 (t80) cc_final: 0.6501 (t80) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.3846 time to fit residues: 24.5913 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 : 0.555 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4838 r_free = 0.4838 target = 0.248557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.198682 restraints weight = 18360.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.200634 restraints weight = 11494.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.201229 restraints weight = 9431.289| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5153 Z= 0.123 Angle : 0.514 9.933 7308 Z= 0.274 Chirality : 0.035 0.162 880 Planarity : 0.004 0.036 671 Dihedral : 23.218 107.487 1526 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.87 % Allowed : 21.87 % 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: 0.09 (0.40), residues: 422 helix: 1.60 (0.38), residues: 178 sheet: -2.27 (0.97), residues: 29 loop : -0.94 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A 644 TYR 0.009 0.002 TYR A 693 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 142) hydrogen bonds : angle 4.37551 ( 392) metal coordination : bond 0.02355 ( 7) metal coordination : angle 2.34203 ( 3) covalent geometry : bond 0.00284 ( 5146) covalent geometry : angle 0.51156 ( 7305) ********************** 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.4172 (m-30) REVERT: A 423 MET cc_start: 0.2468 (mmt) cc_final: 0.1231 (mpp) REVERT: A 706 TYR cc_start: 0.6802 (t80) cc_final: 0.6460 (t80) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.3815 time to fit residues: 22.1079 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4834 r_free = 0.4834 target = 0.248139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.198145 restraints weight = 18491.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.202634 restraints weight = 13080.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.203826 restraints weight = 9683.196| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5153 Z= 0.135 Angle : 0.516 9.558 7308 Z= 0.278 Chirality : 0.036 0.166 880 Planarity : 0.004 0.037 671 Dihedral : 23.221 107.747 1526 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.03 (0.40), residues: 422 helix: 1.58 (0.38), residues: 179 sheet: -2.20 (0.98), residues: 29 loop : -1.02 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.006 0.001 HIS A 328 PHE 0.020 0.002 PHE A 522 TYR 0.011 0.002 TYR A 399 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 142) hydrogen bonds : angle 4.40305 ( 392) metal coordination : bond 0.02376 ( 7) metal coordination : angle 2.31828 ( 3) covalent geometry : bond 0.00312 ( 5146) covalent geometry : angle 0.51445 ( 7305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.18 seconds wall clock time: 73 minutes 56.46 seconds (4436.46 seconds total)