Starting phenix.real_space_refine on Tue Sep 24 00:48:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/09_2024/8e29_27829.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/09_2024/8e29_27829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/09_2024/8e29_27829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/09_2024/8e29_27829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/09_2024/8e29_27829.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/09_2024/8e29_27829.cif" } resolution = 3.1 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 31 5.16 5 C 3821 2.51 5 N 1053 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6197 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5511 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 41, 'TRANS': 650} Chain breaks: 2 Chain: "B" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 686 Classifications: {'RNA': 33} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 27} Time building chain proxies: 4.71, per 1000 atoms: 0.76 Number of scatterers: 6197 At special positions: 0 Unit cell: (77.05, 87.1, 105.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 33 15.00 O 1259 8.00 N 1053 7.00 C 3821 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: 1.65 Conformation dependent library (CDL) restraints added in 859.0 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 30.8% alpha, 23.6% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.734A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.538A pdb=" N ARG A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.645A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.795A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.759A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.709A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.166A pdb=" N PHE A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 765 removed outlier: 3.586A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.096A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP A 97 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 235 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.791A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.822A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.365A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.459A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA8, first strand: chain 'A' and resid 792 through 796 removed outlier: 7.095A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP A 783 " --> pdb=" O MET A 775 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 810 235 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1300 1.33 - 1.45: 1510 1.45 - 1.57: 3468 1.57 - 1.69: 65 1.69 - 1.81: 47 Bond restraints: 6390 Sorted by residual: bond pdb=" CG LEU A 691 " pdb=" CD1 LEU A 691 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.91e+00 bond pdb=" CG LEU A 691 " pdb=" CD2 LEU A 691 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.77e+00 bond pdb=" CB TRP A 468 " pdb=" CG TRP A 468 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.69e+00 bond pdb=" CA SER A 465 " pdb=" CB SER A 465 " ideal model delta sigma weight residual 1.536 1.476 0.060 2.53e-02 1.56e+03 5.60e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8116 1.87 - 3.75: 546 3.75 - 5.62: 105 5.62 - 7.50: 21 7.50 - 9.37: 10 Bond angle restraints: 8798 Sorted by residual: angle pdb=" N ARG A 104 " pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " ideal model delta sigma weight residual 111.84 106.31 5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" N HIS A 688 " pdb=" CA HIS A 688 " pdb=" C HIS A 688 " ideal model delta sigma weight residual 109.46 103.34 6.12 1.66e+00 3.63e-01 1.36e+01 angle pdb=" CA GLU A 512 " pdb=" CB GLU A 512 " pdb=" CG GLU A 512 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" C CYS A 449 " pdb=" N GLU A 450 " pdb=" CA GLU A 450 " ideal model delta sigma weight residual 122.60 117.02 5.58 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N SER A 701 " pdb=" CA SER A 701 " pdb=" C SER A 701 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 ... (remaining 8793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 3567 21.48 - 42.96: 310 42.96 - 64.43: 100 64.43 - 85.91: 18 85.91 - 107.39: 2 Dihedral angle restraints: 3997 sinusoidal: 1967 harmonic: 2030 Sorted by residual: dihedral pdb=" O4' U B 30 " pdb=" C1' U B 30 " pdb=" N1 U B 30 " pdb=" C2 U B 30 " ideal model delta sinusoidal sigma weight residual -160.00 -105.96 -54.04 1 1.50e+01 4.44e-03 1.76e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 672 0.060 - 0.119: 248 0.119 - 0.179: 86 0.179 - 0.238: 11 0.238 - 0.298: 3 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CB VAL A 113 " pdb=" CA VAL A 113 " pdb=" CG1 VAL A 113 " pdb=" CG2 VAL A 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU A 560 " pdb=" CB LEU A 560 " pdb=" CD1 LEU A 560 " pdb=" CD2 LEU A 560 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1017 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 708 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" CG ASP A 708 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASP A 708 " 0.030 2.00e-02 2.50e+03 pdb=" OD2 ASP A 708 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 743 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ARG A 743 " -0.059 2.00e-02 2.50e+03 pdb=" O ARG A 743 " 0.022 2.00e-02 2.50e+03 pdb=" N MET A 744 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 583 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU A 583 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 583 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 584 " -0.019 2.00e-02 2.50e+03 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1796 2.82 - 3.34: 4911 3.34 - 3.86: 9644 3.86 - 4.38: 10585 4.38 - 4.90: 19143 Nonbonded interactions: 46079 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.305 3.040 nonbonded pdb=" O THR A 835 " pdb=" OG SER A 838 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 653 " pdb=" O PHE A 837 " model vdw 2.311 3.040 nonbonded pdb=" O THR A 386 " pdb=" OG1 THR A 386 " model vdw 2.329 3.040 nonbonded pdb=" NH1 ARG A 388 " pdb=" OE2 GLU A 450 " model vdw 2.372 3.120 ... (remaining 46074 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.050 Set scattering table: 0.070 Process input model: 21.230 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.012 0.101 6390 Z= 0.809 Angle : 1.137 9.374 8798 Z= 0.630 Chirality : 0.069 0.298 1020 Planarity : 0.008 0.058 1019 Dihedral : 17.732 107.388 2675 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.66 % Allowed : 6.90 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.29), residues: 686 helix: -1.02 (0.32), residues: 205 sheet: 0.18 (0.41), residues: 155 loop : -1.61 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 468 HIS 0.017 0.002 HIS A 526 PHE 0.049 0.004 PHE A 699 TYR 0.028 0.005 TYR A 853 ARG 0.010 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.738 Fit side-chains REVERT: A 424 ASP cc_start: 0.8112 (t70) cc_final: 0.7877 (t0) REVERT: A 726 ASP cc_start: 0.7801 (p0) cc_final: 0.7515 (t0) REVERT: A 851 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7078 (mp) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2012 time to fit residues: 19.3932 Evaluate side-chains 57 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.0040 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6390 Z= 0.176 Angle : 0.581 8.017 8798 Z= 0.297 Chirality : 0.040 0.138 1020 Planarity : 0.005 0.041 1019 Dihedral : 17.466 108.252 1295 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.82 % Allowed : 11.82 % Favored : 87.36 % 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: -0.55 (0.31), residues: 686 helix: 0.62 (0.36), residues: 214 sheet: 0.35 (0.40), residues: 168 loop : -1.50 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.015 0.001 PHE A 699 TYR 0.011 0.001 TYR A 653 ARG 0.004 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.659 Fit side-chains REVERT: A 803 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7465 (ttp-110) REVERT: A 851 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6953 (mp) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.1844 time to fit residues: 16.4286 Evaluate side-chains 58 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 0.0270 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6390 Z= 0.256 Angle : 0.570 6.951 8798 Z= 0.292 Chirality : 0.040 0.146 1020 Planarity : 0.005 0.041 1019 Dihedral : 17.371 108.764 1290 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.99 % Allowed : 13.63 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.32), residues: 686 helix: 0.99 (0.37), residues: 213 sheet: 0.44 (0.40), residues: 172 loop : -1.48 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 PHE 0.016 0.002 PHE A 699 TYR 0.011 0.002 TYR A 340 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.665 Fit side-chains REVERT: A 803 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7511 (ttp-110) REVERT: A 851 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6877 (mp) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1972 time to fit residues: 15.8790 Evaluate side-chains 58 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 0.0270 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6390 Z= 0.311 Angle : 0.580 6.796 8798 Z= 0.296 Chirality : 0.041 0.150 1020 Planarity : 0.005 0.041 1019 Dihedral : 17.356 107.470 1290 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.81 % Allowed : 14.61 % Favored : 83.58 % 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: -0.28 (0.32), residues: 686 helix: 1.02 (0.37), residues: 212 sheet: 0.53 (0.40), residues: 172 loop : -1.52 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.007 0.001 HIS A 526 PHE 0.016 0.002 PHE A 699 TYR 0.012 0.002 TYR A 340 ARG 0.005 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.728 Fit side-chains REVERT: A 58 ASP cc_start: 0.8244 (t70) cc_final: 0.7996 (t0) REVERT: A 851 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6986 (mp) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.1885 time to fit residues: 15.6765 Evaluate side-chains 58 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6390 Z= 0.177 Angle : 0.505 6.442 8798 Z= 0.258 Chirality : 0.038 0.142 1020 Planarity : 0.004 0.037 1019 Dihedral : 17.241 105.815 1290 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 16.58 % Favored : 82.10 % 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: 686 helix: 1.46 (0.38), residues: 209 sheet: 0.63 (0.41), residues: 172 loop : -1.38 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.010 0.001 PHE A 699 TYR 0.010 0.001 TYR A 674 ARG 0.005 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.721 Fit side-chains REVERT: A 58 ASP cc_start: 0.8251 (t70) cc_final: 0.8030 (t0) REVERT: A 803 ARG cc_start: 0.7547 (ttp-110) cc_final: 0.7328 (ttp-110) REVERT: A 851 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6825 (mp) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.1695 time to fit residues: 15.7118 Evaluate side-chains 61 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6390 Z= 0.250 Angle : 0.540 6.186 8798 Z= 0.276 Chirality : 0.040 0.147 1020 Planarity : 0.004 0.039 1019 Dihedral : 17.159 103.953 1290 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.79 % Allowed : 16.09 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.33), residues: 686 helix: 1.39 (0.38), residues: 212 sheet: 0.71 (0.41), residues: 170 loop : -1.40 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.005 0.001 HIS A 526 PHE 0.013 0.001 PHE A 699 TYR 0.011 0.001 TYR A 674 ARG 0.006 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.693 Fit side-chains REVERT: A 657 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7213 (mtt90) REVERT: A 851 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6881 (mp) outliers start: 17 outliers final: 11 residues processed: 69 average time/residue: 0.1834 time to fit residues: 17.1001 Evaluate side-chains 67 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 0.0170 chunk 41 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6390 Z= 0.140 Angle : 0.485 6.231 8798 Z= 0.249 Chirality : 0.037 0.139 1020 Planarity : 0.004 0.036 1019 Dihedral : 16.921 101.373 1290 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.97 % Allowed : 17.57 % Favored : 80.46 % 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: 0.32 (0.33), residues: 686 helix: 1.78 (0.38), residues: 209 sheet: 0.81 (0.41), residues: 170 loop : -1.29 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.002 0.001 HIS A 526 PHE 0.008 0.001 PHE A 699 TYR 0.008 0.001 TYR A 674 ARG 0.007 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.662 Fit side-chains REVERT: A 657 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7171 (mtt90) REVERT: A 851 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6744 (mp) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1903 time to fit residues: 16.8872 Evaluate side-chains 64 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 66 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6390 Z= 0.181 Angle : 0.509 6.445 8798 Z= 0.258 Chirality : 0.038 0.145 1020 Planarity : 0.004 0.036 1019 Dihedral : 16.853 99.496 1290 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.13 % Allowed : 17.73 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.34), residues: 686 helix: 1.78 (0.38), residues: 209 sheet: 0.85 (0.42), residues: 170 loop : -1.31 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.011 0.001 PHE A 481 TYR 0.009 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.663 Fit side-chains REVERT: A 657 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7146 (mtt90) REVERT: A 803 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7159 (ttp-110) REVERT: A 851 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6744 (mp) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 0.1815 time to fit residues: 15.9944 Evaluate side-chains 68 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.0000 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6390 Z= 0.153 Angle : 0.496 7.110 8798 Z= 0.251 Chirality : 0.038 0.141 1020 Planarity : 0.004 0.035 1019 Dihedral : 16.760 97.039 1290 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.97 % Allowed : 17.73 % Favored : 80.30 % 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: 0.42 (0.33), residues: 686 helix: 1.86 (0.38), residues: 209 sheet: 0.90 (0.42), residues: 170 loop : -1.26 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.003 0.001 HIS A 562 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.632 Fit side-chains REVERT: A 657 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6693 (mmt90) REVERT: A 803 ARG cc_start: 0.7396 (ttp-110) cc_final: 0.7113 (ttp-110) REVERT: A 851 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6694 (mp) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.1945 time to fit residues: 17.5060 Evaluate side-chains 65 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6390 Z= 0.157 Angle : 0.498 7.321 8798 Z= 0.253 Chirality : 0.038 0.144 1020 Planarity : 0.004 0.035 1019 Dihedral : 16.670 94.214 1290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.13 % Allowed : 17.57 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.33), residues: 686 helix: 1.91 (0.38), residues: 209 sheet: 0.93 (0.42), residues: 170 loop : -1.26 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.703 Fit side-chains REVERT: A 657 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6737 (mmt90) REVERT: A 803 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.7076 (ttp-110) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1866 time to fit residues: 17.1141 Evaluate side-chains 67 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121112 restraints weight = 6527.298| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.11 r_work: 0.3314 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6390 Z= 0.139 Angle : 0.493 7.240 8798 Z= 0.249 Chirality : 0.037 0.142 1020 Planarity : 0.004 0.035 1019 Dihedral : 16.540 94.558 1288 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.97 % Allowed : 18.06 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.34), residues: 686 helix: 2.01 (0.38), residues: 209 sheet: 0.98 (0.42), residues: 170 loop : -1.19 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 526 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1644.16 seconds wall clock time: 30 minutes 4.74 seconds (1804.74 seconds total)