Starting phenix.real_space_refine on Thu Nov 14 11:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/11_2024/8ooy_17033.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/11_2024/8ooy_17033.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/11_2024/8ooy_17033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/11_2024/8ooy_17033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/11_2024/8ooy_17033.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/11_2024/8ooy_17033.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= 0.000 sd= 0.001 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 51 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3520 2.51 5 N 1029 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4782 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Chain: "T" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.76 Number of scatterers: 5828 At special positions: 0 Unit cell: (89.452, 96.14, 78.584, 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 15 16.00 P 51 15.00 Mg 1 11.99 O 1212 8.00 N 1029 7.00 C 3520 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: 1.79 Conformation dependent library (CDL) restraints added in 807.0 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 62.7% alpha, 5.6% beta 23 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.673A pdb=" N LYS A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.604A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.605A pdb=" N ASP A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.944A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.045A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.647A pdb=" N GLN A 488 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 519 Proline residue: A 514 - end of helix removed outlier: 3.555A pdb=" N HIS A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.405A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.831A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.628A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.032A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 636 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.799A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 removed outlier: 3.877A pdb=" N ILE A 679 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 745 through 749 Processing helix chain 'A' and resid 750 through 767 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 795 through 812 removed outlier: 3.734A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 871 removed outlier: 3.743A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.570A pdb=" N ALA A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.620A pdb=" N TYR A 382 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.262A pdb=" N PHE A 352 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.587A pdb=" N SER A 670 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 699 through 702 252 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.04 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: 1534 1.33 - 1.45: 1226 1.45 - 1.57: 3153 1.57 - 1.69: 99 1.69 - 1.81: 29 Bond restraints: 6041 Sorted by residual: bond pdb=" N VAL A 663 " pdb=" CA VAL A 663 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.48e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.88e+00 bond pdb=" N VAL A 504 " pdb=" CA VAL A 504 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.17e-02 7.31e+03 5.56e+00 bond pdb=" N ASP A 501 " pdb=" CA ASP A 501 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.41e+00 bond pdb=" N THR A 485 " pdb=" CA THR A 485 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.25e-02 6.40e+03 4.83e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 8061 1.55 - 3.09: 273 3.09 - 4.64: 44 4.64 - 6.18: 7 6.18 - 7.73: 6 Bond angle restraints: 8391 Sorted by residual: angle pdb=" CA THR A 664 " pdb=" C THR A 664 " pdb=" O THR A 664 " ideal model delta sigma weight residual 121.56 117.76 3.80 1.09e+00 8.42e-01 1.21e+01 angle pdb=" CA LEU A 506 " pdb=" C LEU A 506 " pdb=" O LEU A 506 " ideal model delta sigma weight residual 120.90 117.30 3.60 1.07e+00 8.73e-01 1.13e+01 angle pdb=" C ASN A 554 " pdb=" N HIS A 555 " pdb=" CA HIS A 555 " ideal model delta sigma weight residual 120.28 125.04 -4.76 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 112.12 109.38 2.74 8.40e-01 1.42e+00 1.06e+01 angle pdb=" N THR A 505 " pdb=" CA THR A 505 " pdb=" C THR A 505 " ideal model delta sigma weight residual 111.11 107.33 3.78 1.20e+00 6.94e-01 9.94e+00 ... (remaining 8386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2879 17.28 - 34.57: 390 34.57 - 51.85: 194 51.85 - 69.13: 65 69.13 - 86.41: 7 Dihedral angle restraints: 3535 sinusoidal: 1772 harmonic: 1763 Sorted by residual: dihedral pdb=" CA VAL A 815 " pdb=" C VAL A 815 " pdb=" N GLU A 816 " pdb=" CA GLU A 816 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP A 892 " pdb=" CB ASP A 892 " pdb=" CG ASP A 892 " pdb=" OD1 ASP A 892 " ideal model delta sinusoidal sigma weight residual -30.00 -85.98 55.98 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " pdb=" CD GLU A 917 " pdb=" OE1 GLU A 917 " ideal model delta sinusoidal sigma weight residual 0.00 86.41 -86.41 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 694 0.042 - 0.083: 179 0.083 - 0.125: 64 0.125 - 0.167: 5 0.167 - 0.208: 2 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 779 " pdb=" N ILE A 779 " pdb=" C ILE A 779 " pdb=" CB ILE A 779 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 941 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 521 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 522 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 779 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 780 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 901 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C HIS A 901 " 0.026 2.00e-02 2.50e+03 pdb=" O HIS A 901 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 902 " -0.009 2.00e-02 2.50e+03 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5044 3.17 - 3.75: 10010 3.75 - 4.32: 13143 4.32 - 4.90: 20807 Nonbonded interactions: 49064 Sorted by model distance: nonbonded pdb=" OD1 ASP A 355 " pdb="MG MG A1001 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.201 3.120 nonbonded pdb=" NE2 HIS A 555 " pdb=" OE2 GLU A 685 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLU A 729 " pdb=" NZ LYS A 731 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 817 " pdb=" OG1 THR A 851 " model vdw 2.231 3.040 ... (remaining 49059 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: 1.560 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.530 Find NCS groups from input model: 0.060 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.004 0.039 6041 Z= 0.219 Angle : 0.681 7.727 8391 Z= 0.395 Chirality : 0.043 0.208 944 Planarity : 0.004 0.045 913 Dihedral : 20.016 86.412 2395 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.79 % Allowed : 0.39 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.97 (0.35), residues: 602 helix: 0.59 (0.30), residues: 315 sheet: -3.34 (0.66), residues: 47 loop : -1.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 465 HIS 0.011 0.001 HIS A 555 PHE 0.016 0.002 PHE A 354 TYR 0.015 0.001 TYR A 814 ARG 0.006 0.001 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 679 ILE cc_start: 0.8365 (mm) cc_final: 0.8088 (mm) REVERT: A 848 MET cc_start: 0.7810 (mmm) cc_final: 0.7187 (mmm) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1628 time to fit residues: 16.9970 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 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 507 GLN ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6041 Z= 0.207 Angle : 0.613 8.178 8391 Z= 0.330 Chirality : 0.041 0.191 944 Planarity : 0.005 0.054 913 Dihedral : 21.779 66.149 1200 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.38 % Allowed : 7.28 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.63 (0.35), residues: 602 helix: 0.85 (0.29), residues: 325 sheet: -3.29 (0.64), residues: 49 loop : -1.57 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 342 HIS 0.007 0.001 HIS A 555 PHE 0.019 0.001 PHE A 886 TYR 0.020 0.001 TYR A 814 ARG 0.004 0.001 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8369 (mt) cc_final: 0.8080 (mt) REVERT: A 449 LEU cc_start: 0.8867 (mt) cc_final: 0.8659 (mt) REVERT: A 506 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 661 GLN cc_start: 0.8661 (tt0) cc_final: 0.8408 (tt0) REVERT: A 679 ILE cc_start: 0.8523 (mm) cc_final: 0.8249 (mm) REVERT: A 848 MET cc_start: 0.7734 (mmm) cc_final: 0.7199 (mmm) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.1516 time to fit residues: 14.5884 Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6041 Z= 0.185 Angle : 0.576 7.745 8391 Z= 0.310 Chirality : 0.039 0.164 944 Planarity : 0.005 0.051 913 Dihedral : 21.734 64.056 1200 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.77 % Allowed : 11.22 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.29 (0.35), residues: 602 helix: 1.08 (0.29), residues: 326 sheet: -3.08 (0.66), residues: 48 loop : -1.35 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 866 HIS 0.005 0.001 HIS A 555 PHE 0.016 0.002 PHE A 886 TYR 0.018 0.001 TYR A 814 ARG 0.004 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8386 (mt) cc_final: 0.8084 (mt) REVERT: A 506 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8378 (mm) REVERT: A 661 GLN cc_start: 0.8703 (tt0) cc_final: 0.8434 (tt0) REVERT: A 679 ILE cc_start: 0.8509 (mm) cc_final: 0.8263 (mm) REVERT: A 783 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 788 MET cc_start: 0.7466 (mtm) cc_final: 0.7104 (mtm) REVERT: A 789 ASP cc_start: 0.7764 (m-30) cc_final: 0.7270 (t0) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1697 time to fit residues: 16.5222 Evaluate side-chains 65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6041 Z= 0.189 Angle : 0.569 8.099 8391 Z= 0.307 Chirality : 0.039 0.153 944 Planarity : 0.004 0.049 913 Dihedral : 21.781 64.725 1200 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.35), residues: 602 helix: 1.15 (0.29), residues: 326 sheet: -3.13 (0.62), residues: 48 loop : -1.32 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 866 HIS 0.003 0.001 HIS A 555 PHE 0.014 0.002 PHE A 886 TYR 0.017 0.001 TYR A 814 ARG 0.004 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8382 (mt) cc_final: 0.8126 (mt) REVERT: A 506 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 679 ILE cc_start: 0.8570 (mm) cc_final: 0.8346 (mm) REVERT: A 755 ARG cc_start: 0.8284 (ppt170) cc_final: 0.7906 (ppt170) REVERT: A 783 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 788 MET cc_start: 0.7535 (mtm) cc_final: 0.7292 (mtm) REVERT: A 789 ASP cc_start: 0.7697 (m-30) cc_final: 0.7248 (t0) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 0.1740 time to fit residues: 16.7797 Evaluate side-chains 66 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 54 optimal weight: 0.0370 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6041 Z= 0.211 Angle : 0.579 7.743 8391 Z= 0.309 Chirality : 0.040 0.160 944 Planarity : 0.004 0.048 913 Dihedral : 21.841 69.269 1200 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.17 % Allowed : 15.35 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.36), residues: 602 helix: 1.13 (0.29), residues: 327 sheet: -3.23 (0.61), residues: 48 loop : -1.27 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 342 HIS 0.003 0.001 HIS A 901 PHE 0.016 0.002 PHE A 792 TYR 0.017 0.002 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8333 (mm) REVERT: A 614 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7778 (mm) REVERT: A 679 ILE cc_start: 0.8603 (mm) cc_final: 0.8389 (mm) REVERT: A 755 ARG cc_start: 0.8297 (ppt170) cc_final: 0.7902 (ppt170) REVERT: A 788 MET cc_start: 0.7528 (mtm) cc_final: 0.7309 (mtm) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.1718 time to fit residues: 16.8962 Evaluate side-chains 65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.0040 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6041 Z= 0.174 Angle : 0.570 7.798 8391 Z= 0.305 Chirality : 0.039 0.178 944 Planarity : 0.004 0.048 913 Dihedral : 21.850 70.769 1200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.95 % Allowed : 15.35 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.35), residues: 602 helix: 1.17 (0.29), residues: 328 sheet: -2.94 (0.61), residues: 47 loop : -1.24 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 342 HIS 0.003 0.001 HIS A 555 PHE 0.019 0.001 PHE A 792 TYR 0.015 0.001 TYR A 814 ARG 0.005 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 614 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7806 (mm) REVERT: A 668 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7342 (mtp180) REVERT: A 679 ILE cc_start: 0.8573 (mm) cc_final: 0.8367 (mm) REVERT: A 755 ARG cc_start: 0.8290 (ppt170) cc_final: 0.7908 (ppt170) outliers start: 15 outliers final: 7 residues processed: 79 average time/residue: 0.1794 time to fit residues: 19.0843 Evaluate side-chains 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN A 761 ASN A 776 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6041 Z= 0.302 Angle : 0.672 11.786 8391 Z= 0.347 Chirality : 0.043 0.185 944 Planarity : 0.005 0.047 913 Dihedral : 21.975 75.001 1200 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.95 % Allowed : 17.52 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.29 (0.35), residues: 602 helix: 0.99 (0.29), residues: 326 sheet: -2.93 (0.60), residues: 47 loop : -1.26 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 465 HIS 0.005 0.001 HIS A 901 PHE 0.019 0.002 PHE A 792 TYR 0.019 0.002 TYR A 814 ARG 0.004 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8398 (mt) cc_final: 0.8091 (mt) REVERT: A 506 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 679 ILE cc_start: 0.8777 (mm) cc_final: 0.8530 (mm) REVERT: A 755 ARG cc_start: 0.8327 (ppt170) cc_final: 0.8056 (ppt170) REVERT: A 848 MET cc_start: 0.7837 (mmm) cc_final: 0.7025 (mmm) outliers start: 15 outliers final: 9 residues processed: 67 average time/residue: 0.1901 time to fit residues: 17.3739 Evaluate side-chains 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7741 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6041 Z= 0.202 Angle : 0.628 11.579 8391 Z= 0.325 Chirality : 0.041 0.171 944 Planarity : 0.004 0.048 913 Dihedral : 21.904 75.629 1200 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.17 % Allowed : 17.52 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.14 (0.35), residues: 602 helix: 1.09 (0.29), residues: 327 sheet: -2.87 (0.60), residues: 47 loop : -1.15 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 866 HIS 0.003 0.001 HIS A 901 PHE 0.021 0.002 PHE A 792 TYR 0.016 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8397 (mt) cc_final: 0.8070 (mt) REVERT: A 506 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 679 ILE cc_start: 0.8772 (mm) cc_final: 0.8534 (mm) REVERT: A 755 ARG cc_start: 0.8318 (ppt170) cc_final: 0.8020 (ppt170) REVERT: A 768 MET cc_start: 0.7518 (ppp) cc_final: 0.6853 (ppp) REVERT: A 848 MET cc_start: 0.7752 (mmm) cc_final: 0.7074 (mmm) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1666 time to fit residues: 15.1812 Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6041 Z= 0.196 Angle : 0.625 11.229 8391 Z= 0.323 Chirality : 0.040 0.176 944 Planarity : 0.004 0.048 913 Dihedral : 21.821 76.883 1200 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.77 % Allowed : 18.70 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.02 (0.35), residues: 602 helix: 1.16 (0.29), residues: 327 sheet: -2.64 (0.61), residues: 47 loop : -1.09 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 513 HIS 0.003 0.001 HIS A 901 PHE 0.024 0.002 PHE A 792 TYR 0.015 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8407 (mt) cc_final: 0.8103 (mt) REVERT: A 506 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 668 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7372 (mtp180) REVERT: A 679 ILE cc_start: 0.8771 (mm) cc_final: 0.8536 (mm) REVERT: A 755 ARG cc_start: 0.8303 (ppt170) cc_final: 0.8042 (ppt170) REVERT: A 768 MET cc_start: 0.7647 (ppp) cc_final: 0.6920 (ppp) REVERT: A 848 MET cc_start: 0.7703 (mmm) cc_final: 0.7100 (mmm) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1933 time to fit residues: 15.8842 Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6041 Z= 0.210 Angle : 0.627 11.115 8391 Z= 0.327 Chirality : 0.040 0.161 944 Planarity : 0.004 0.047 913 Dihedral : 21.841 78.332 1200 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.56 % Allowed : 17.52 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.35), residues: 602 helix: 1.11 (0.29), residues: 328 sheet: -2.57 (0.64), residues: 47 loop : -1.08 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 342 HIS 0.003 0.001 HIS A 901 PHE 0.016 0.002 PHE A 792 TYR 0.015 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8394 (mt) cc_final: 0.8078 (mt) REVERT: A 506 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 668 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7374 (mtp180) REVERT: A 679 ILE cc_start: 0.8806 (mm) cc_final: 0.8584 (mm) REVERT: A 768 MET cc_start: 0.7632 (ppp) cc_final: 0.6954 (ppp) REVERT: A 848 MET cc_start: 0.7760 (mmm) cc_final: 0.7117 (mmm) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.1923 time to fit residues: 16.3965 Evaluate side-chains 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 20 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.106410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085110 restraints weight = 14620.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085352 restraints weight = 11547.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086269 restraints weight = 10462.946| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6041 Z= 0.176 Angle : 0.613 10.951 8391 Z= 0.318 Chirality : 0.040 0.170 944 Planarity : 0.004 0.048 913 Dihedral : 21.780 79.449 1200 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.97 % Allowed : 17.91 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.10 (0.35), residues: 602 helix: 1.18 (0.29), residues: 328 sheet: -2.50 (0.65), residues: 47 loop : -0.93 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 513 HIS 0.002 0.001 HIS A 555 PHE 0.016 0.001 PHE A 886 TYR 0.013 0.001 TYR A 814 ARG 0.005 0.000 ARG A 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1362.45 seconds wall clock time: 25 minutes 27.22 seconds (1527.22 seconds total)