Starting phenix.real_space_refine on Fri Dec 27 15:42:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmf_27535/12_2024/8dmf_27535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmf_27535/12_2024/8dmf_27535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmf_27535/12_2024/8dmf_27535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmf_27535/12_2024/8dmf_27535.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmf_27535/12_2024/8dmf_27535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmf_27535/12_2024/8dmf_27535.cif" } resolution = 4.0 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= -0.001 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3589 2.51 5 N 951 2.21 5 O 1093 1.98 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-5532/modules/chem_data/mon_lib" Total number of atoms: 5670 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5637 Classifications: {'peptide': 718} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 685} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.11, per 1000 atoms: 0.72 Number of scatterers: 5670 At special positions: 0 Unit cell: (75.828, 72.624, 127.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 3 15.00 Mg 1 11.99 O 1093 8.00 N 951 7.00 C 3589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 895.1 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 31.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.531A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.626A pdb=" N THR A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.627A pdb=" N GLY A 170 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 220 Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.231A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.534A pdb=" N PHE A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.512A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 removed outlier: 3.553A pdb=" N GLN A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 6.834A pdb=" N LYS A 10 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 79 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 12 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 101 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU A 132 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 103 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN A 134 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 105 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 159 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N CYS A 256 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164 Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343 removed outlier: 6.964A pdb=" N SER A 302 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.510A pdb=" N LEU A 361 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350 removed outlier: 4.477A pdb=" N ILE A 347 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.585A pdb=" N GLN A 439 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 440 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 400 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA8, first strand: chain 'A' and resid 482 through 488 removed outlier: 3.539A pdb=" N ALA A 482 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU A 500 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 590 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS A 502 " --> pdb=" O TYR A 588 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 542 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 585 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 544 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 587 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 654 removed outlier: 6.706A pdb=" N VAL A 664 " --> pdb=" O MET A 652 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET A 654 " --> pdb=" O LYS A 662 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 662 " --> pdb=" O MET A 654 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1743 1.33 - 1.45: 846 1.45 - 1.57: 3124 1.57 - 1.69: 5 1.69 - 1.81: 61 Bond restraints: 5779 Sorted by residual: bond pdb=" N GLU A 476 " pdb=" CA GLU A 476 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.25e-02 6.40e+03 7.96e+00 bond pdb=" N GLU A 697 " pdb=" CA GLU A 697 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.32e-02 5.74e+03 6.38e+00 bond pdb=" N TYR A 474 " pdb=" CA TYR A 474 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.22e-02 6.72e+03 6.21e+00 bond pdb=" N LYS A 22 " pdb=" CA LYS A 22 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.22e-02 6.72e+03 6.10e+00 bond pdb=" N SER A 695 " pdb=" CA SER A 695 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.21e-02 6.83e+03 5.63e+00 ... (remaining 5774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 7554 1.63 - 3.26: 201 3.26 - 4.89: 30 4.89 - 6.52: 5 6.52 - 8.15: 5 Bond angle restraints: 7795 Sorted by residual: angle pdb=" N GLU A 425 " pdb=" CA GLU A 425 " pdb=" C GLU A 425 " ideal model delta sigma weight residual 111.28 107.47 3.81 1.09e+00 8.42e-01 1.22e+01 angle pdb=" CA GLU A 697 " pdb=" C GLU A 697 " pdb=" O GLU A 697 " ideal model delta sigma weight residual 121.36 118.00 3.36 1.06e+00 8.90e-01 1.00e+01 angle pdb=" N GLU A 424 " pdb=" CA GLU A 424 " pdb=" C GLU A 424 " ideal model delta sigma weight residual 111.71 108.17 3.54 1.15e+00 7.56e-01 9.47e+00 angle pdb=" CA GLU A 476 " pdb=" C GLU A 476 " pdb=" O GLU A 476 " ideal model delta sigma weight residual 121.82 118.12 3.70 1.21e+00 6.83e-01 9.36e+00 angle pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" O TYR A 696 " ideal model delta sigma weight residual 121.55 118.32 3.23 1.06e+00 8.90e-01 9.28e+00 ... (remaining 7790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 3265 22.34 - 44.68: 233 44.68 - 67.02: 10 67.02 - 89.36: 3 89.36 - 111.70: 4 Dihedral angle restraints: 3515 sinusoidal: 1461 harmonic: 2054 Sorted by residual: dihedral pdb=" C8 GTP A 802 " pdb=" C1' GTP A 802 " pdb=" N9 GTP A 802 " pdb=" O4' GTP A 802 " ideal model delta sinusoidal sigma weight residual 104.59 -7.11 111.70 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" C5' GTP A 802 " pdb=" O5' GTP A 802 " pdb=" PA GTP A 802 " pdb=" O3A GTP A 802 " ideal model delta sinusoidal sigma weight residual 69.27 178.40 -109.13 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" CA MET A 224 " pdb=" C MET A 224 " pdb=" N GLU A 225 " pdb=" CA GLU A 225 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 3512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 573 0.037 - 0.073: 172 0.073 - 0.110: 76 0.110 - 0.146: 22 0.146 - 0.183: 3 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA GLU A 424 " pdb=" N GLU A 424 " pdb=" C GLU A 424 " pdb=" CB GLU A 424 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA ARG A 423 " pdb=" N ARG A 423 " pdb=" C ARG A 423 " pdb=" CB ARG A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 843 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 632 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 633 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 276 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 277 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 21 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C GLY A 21 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY A 21 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS A 22 " -0.006 2.00e-02 2.50e+03 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 65 2.56 - 3.15: 4775 3.15 - 3.73: 9308 3.73 - 4.32: 11920 4.32 - 4.90: 19654 Nonbonded interactions: 45722 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O3A GTP A 802 " model vdw 1.977 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G GTP A 802 " model vdw 2.168 2.170 nonbonded pdb=" N THR A 23 " pdb="MG MG A 801 " model vdw 2.183 2.250 nonbonded pdb=" OH TYR A 400 " pdb=" NH2 ARG A 402 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS A 291 " pdb=" OH TYR A 388 " model vdw 2.267 3.120 ... (remaining 45717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.003 0.035 5779 Z= 0.195 Angle : 0.636 8.154 7795 Z= 0.347 Chirality : 0.046 0.183 846 Planarity : 0.004 0.042 1012 Dihedral : 14.277 111.705 2203 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 (0.33), residues: 716 helix: 1.11 (0.39), residues: 202 sheet: -0.03 (0.41), residues: 195 loop : -0.97 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 455 HIS 0.009 0.001 HIS A 449 PHE 0.011 0.001 PHE A 610 TYR 0.008 0.001 TYR A 696 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.8795 (ptm) cc_final: 0.8594 (ttt) REVERT: A 251 MET cc_start: 0.8929 (tmm) cc_final: 0.8647 (tmm) REVERT: A 263 MET cc_start: 0.8783 (mmp) cc_final: 0.8097 (mmp) REVERT: A 323 MET cc_start: 0.8461 (mmp) cc_final: 0.8205 (mmm) REVERT: A 563 MET cc_start: 0.9575 (mmp) cc_final: 0.9122 (mmm) REVERT: A 650 MET cc_start: 0.9167 (mpp) cc_final: 0.8874 (mpp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1548 time to fit residues: 10.4638 Evaluate side-chains 36 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 36 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 443 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5779 Z= 0.161 Angle : 0.605 10.196 7795 Z= 0.301 Chirality : 0.045 0.139 846 Planarity : 0.004 0.038 1012 Dihedral : 7.572 111.381 787 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.33 % Allowed : 8.32 % Favored : 91.35 % 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: -0.16 (0.32), residues: 716 helix: 1.29 (0.37), residues: 206 sheet: -0.11 (0.40), residues: 199 loop : -1.00 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.008 0.001 HIS A 449 PHE 0.011 0.001 PHE A 255 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.711 Fit side-chains REVERT: A 206 MET cc_start: 0.9313 (mmp) cc_final: 0.9017 (mmt) REVERT: A 263 MET cc_start: 0.8648 (mmp) cc_final: 0.7983 (mmp) REVERT: A 303 LEU cc_start: 0.9306 (mt) cc_final: 0.9036 (mt) REVERT: A 323 MET cc_start: 0.8447 (mmp) cc_final: 0.8167 (mmm) REVERT: A 389 LYS cc_start: 0.8626 (pttm) cc_final: 0.8088 (tppt) REVERT: A 394 LYS cc_start: 0.9216 (tppt) cc_final: 0.8960 (tptp) REVERT: A 563 MET cc_start: 0.9417 (mmp) cc_final: 0.9076 (mmm) REVERT: A 650 MET cc_start: 0.9109 (mpp) cc_final: 0.8714 (mpp) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1791 time to fit residues: 11.0754 Evaluate side-chains 39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 22 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5779 Z= 0.162 Angle : 0.577 9.468 7795 Z= 0.284 Chirality : 0.044 0.164 846 Planarity : 0.003 0.034 1012 Dihedral : 7.281 106.400 787 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.98 % Allowed : 10.77 % Favored : 88.25 % 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: 0.01 (0.32), residues: 716 helix: 1.51 (0.37), residues: 207 sheet: -0.02 (0.40), residues: 199 loop : -0.98 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 429 HIS 0.006 0.001 HIS A 449 PHE 0.010 0.001 PHE A 255 TYR 0.010 0.001 TYR A 121 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.9254 (mtm) cc_final: 0.9039 (mpp) REVERT: A 206 MET cc_start: 0.9340 (mmp) cc_final: 0.9057 (mmt) REVERT: A 263 MET cc_start: 0.8553 (mmp) cc_final: 0.7820 (mmp) REVERT: A 303 LEU cc_start: 0.9328 (mt) cc_final: 0.9111 (mt) REVERT: A 389 LYS cc_start: 0.8649 (pttm) cc_final: 0.8029 (tppt) REVERT: A 394 LYS cc_start: 0.9215 (tppt) cc_final: 0.8993 (tptp) REVERT: A 563 MET cc_start: 0.9343 (mmp) cc_final: 0.9072 (mmm) REVERT: A 567 MET cc_start: 0.9318 (mpp) cc_final: 0.9079 (mpp) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.1666 time to fit residues: 10.4885 Evaluate side-chains 43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 overall best weight: 5.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5779 Z= 0.236 Angle : 0.593 8.420 7795 Z= 0.297 Chirality : 0.043 0.137 846 Planarity : 0.004 0.033 1012 Dihedral : 7.478 108.462 787 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.14 % Allowed : 12.40 % Favored : 86.46 % 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: 0.08 (0.32), residues: 716 helix: 1.57 (0.37), residues: 207 sheet: 0.11 (0.40), residues: 192 loop : -0.99 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.005 0.001 HIS A 449 PHE 0.012 0.001 PHE A 255 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9305 (mmp) cc_final: 0.8981 (mmt) REVERT: A 251 MET cc_start: 0.8588 (tmm) cc_final: 0.8158 (tmm) REVERT: A 263 MET cc_start: 0.8804 (mmp) cc_final: 0.8051 (mmp) REVERT: A 323 MET cc_start: 0.8773 (mmm) cc_final: 0.8351 (mmm) REVERT: A 394 LYS cc_start: 0.9263 (tppt) cc_final: 0.9061 (tptp) REVERT: A 422 MET cc_start: 0.9520 (mmm) cc_final: 0.9247 (mmm) REVERT: A 563 MET cc_start: 0.9402 (mmp) cc_final: 0.9070 (mmm) REVERT: A 567 MET cc_start: 0.9297 (mpp) cc_final: 0.9072 (mpp) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.1692 time to fit residues: 10.1576 Evaluate side-chains 42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5779 Z= 0.241 Angle : 0.599 8.428 7795 Z= 0.297 Chirality : 0.043 0.138 846 Planarity : 0.004 0.033 1012 Dihedral : 7.516 108.506 787 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.47 % Allowed : 13.05 % Favored : 85.48 % 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 (0.32), residues: 716 helix: 1.58 (0.37), residues: 207 sheet: 0.04 (0.42), residues: 185 loop : -1.06 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 429 HIS 0.005 0.001 HIS A 449 PHE 0.016 0.001 PHE A 255 TYR 0.013 0.001 TYR A 626 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9201 (mmp) cc_final: 0.8953 (mmp) REVERT: A 251 MET cc_start: 0.8588 (tmm) cc_final: 0.8226 (tmm) REVERT: A 323 MET cc_start: 0.8743 (mmm) cc_final: 0.8281 (mmm) REVERT: A 422 MET cc_start: 0.9542 (mmm) cc_final: 0.9231 (mmm) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.1593 time to fit residues: 9.9619 Evaluate side-chains 43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5779 Z= 0.249 Angle : 0.609 8.433 7795 Z= 0.302 Chirality : 0.043 0.149 846 Planarity : 0.004 0.034 1012 Dihedral : 7.537 108.254 787 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.47 % Allowed : 14.52 % Favored : 84.01 % 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 (0.33), residues: 716 helix: 1.63 (0.37), residues: 207 sheet: 0.10 (0.43), residues: 184 loop : -1.14 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 429 HIS 0.005 0.001 HIS A 449 PHE 0.012 0.001 PHE A 255 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9154 (mmp) cc_final: 0.8922 (mmp) REVERT: A 251 MET cc_start: 0.8565 (tmm) cc_final: 0.8239 (tmm) REVERT: A 323 MET cc_start: 0.8732 (mmm) cc_final: 0.8456 (mmm) REVERT: A 422 MET cc_start: 0.9580 (mmm) cc_final: 0.9255 (mmm) REVERT: A 566 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9343 (mm) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.1490 time to fit residues: 9.5196 Evaluate side-chains 42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5779 Z= 0.380 Angle : 0.705 8.705 7795 Z= 0.356 Chirality : 0.044 0.142 846 Planarity : 0.004 0.038 1012 Dihedral : 8.018 111.129 787 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.63 % Allowed : 16.31 % Favored : 82.06 % 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 (0.32), residues: 716 helix: 1.12 (0.36), residues: 207 sheet: -0.13 (0.42), residues: 184 loop : -1.23 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 429 HIS 0.005 0.002 HIS A 502 PHE 0.020 0.002 PHE A 525 TYR 0.018 0.002 TYR A 626 ARG 0.002 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 206 MET cc_start: 0.9162 (mmp) cc_final: 0.8869 (mmt) REVERT: A 251 MET cc_start: 0.8677 (tmm) cc_final: 0.8344 (tmm) REVERT: A 323 MET cc_start: 0.8716 (mmm) cc_final: 0.8179 (mmm) REVERT: A 672 MET cc_start: 0.9372 (mmm) cc_final: 0.9167 (mmm) outliers start: 10 outliers final: 4 residues processed: 44 average time/residue: 0.1690 time to fit residues: 10.5517 Evaluate side-chains 40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 62 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 27 optimal weight: 0.0870 chunk 50 optimal weight: 6.9990 overall best weight: 2.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5779 Z= 0.164 Angle : 0.615 8.775 7795 Z= 0.299 Chirality : 0.044 0.142 846 Planarity : 0.003 0.032 1012 Dihedral : 7.240 104.674 787 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.65 % Allowed : 17.46 % Favored : 81.89 % 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: -0.05 (0.33), residues: 716 helix: 1.65 (0.38), residues: 207 sheet: -0.03 (0.44), residues: 168 loop : -1.11 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.005 0.001 HIS A 449 PHE 0.010 0.001 PHE A 255 TYR 0.011 0.001 TYR A 626 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.9326 (mtm) cc_final: 0.9111 (mtm) REVERT: A 251 MET cc_start: 0.8486 (tmm) cc_final: 0.8199 (tmm) REVERT: A 269 MET cc_start: 0.9557 (mmt) cc_final: 0.9332 (mmp) REVERT: A 303 LEU cc_start: 0.9339 (mt) cc_final: 0.9039 (mt) REVERT: A 323 MET cc_start: 0.8692 (mmm) cc_final: 0.8379 (mmm) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1574 time to fit residues: 9.8036 Evaluate side-chains 40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5779 Z= 0.256 Angle : 0.672 10.511 7795 Z= 0.329 Chirality : 0.044 0.193 846 Planarity : 0.003 0.033 1012 Dihedral : 7.445 106.310 787 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.98 % Allowed : 17.94 % Favored : 81.08 % 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 (0.32), residues: 716 helix: 1.44 (0.38), residues: 207 sheet: -0.18 (0.42), residues: 179 loop : -1.13 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 429 HIS 0.004 0.001 HIS A 449 PHE 0.013 0.001 PHE A 525 TYR 0.012 0.001 TYR A 626 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8583 (tmm) cc_final: 0.8256 (tmm) REVERT: A 323 MET cc_start: 0.8757 (mmm) cc_final: 0.8192 (mmm) outliers start: 6 outliers final: 2 residues processed: 40 average time/residue: 0.1537 time to fit residues: 9.3231 Evaluate side-chains 37 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 7.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5779 Z= 0.295 Angle : 0.716 10.491 7795 Z= 0.351 Chirality : 0.045 0.184 846 Planarity : 0.004 0.032 1012 Dihedral : 7.654 108.242 787 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.65 % Allowed : 18.60 % Favored : 80.75 % 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: -0.37 (0.32), residues: 716 helix: 1.17 (0.37), residues: 206 sheet: -0.22 (0.42), residues: 179 loop : -1.14 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.004 0.002 HIS A 502 PHE 0.016 0.002 PHE A 525 TYR 0.014 0.001 TYR A 626 ARG 0.002 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9365 (mm) REVERT: A 202 MET cc_start: 0.9001 (tpp) cc_final: 0.8190 (mmm) REVERT: A 251 MET cc_start: 0.8594 (tmm) cc_final: 0.8276 (tmm) REVERT: A 323 MET cc_start: 0.8756 (mmm) cc_final: 0.8195 (mmm) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1545 time to fit residues: 8.7811 Evaluate side-chains 38 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030654 restraints weight = 48072.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.031670 restraints weight = 29352.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032437 restraints weight = 20706.165| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5779 Z= 0.259 Angle : 0.702 12.340 7795 Z= 0.340 Chirality : 0.044 0.166 846 Planarity : 0.003 0.033 1012 Dihedral : 7.529 107.196 787 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.49 % Allowed : 18.76 % Favored : 80.75 % 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: -0.36 (0.32), residues: 716 helix: 1.16 (0.37), residues: 206 sheet: -0.27 (0.42), residues: 175 loop : -1.08 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 429 HIS 0.004 0.001 HIS A 449 PHE 0.013 0.001 PHE A 525 TYR 0.013 0.001 TYR A 626 ARG 0.002 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1092.99 seconds wall clock time: 21 minutes 16.79 seconds (1276.79 seconds total)