Starting phenix.real_space_refine on Tue Feb 11 17:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e29_27829/02_2025/8e29_27829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e29_27829/02_2025/8e29_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/cci-nas-00/data/ceres_data/8e29_27829/02_2025/8e29_27829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e29_27829/02_2025/8e29_27829.map" model { file = "/net/cci-nas-00/data/ceres_data/8e29_27829/02_2025/8e29_27829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e29_27829/02_2025/8e29_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-5592/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: 4.61, per 1000 atoms: 0.74 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: 1.47 Conformation dependent library (CDL) restraints added in 868.5 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: 2.12 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: 2.30 Time building geometry restraints manager: 1.73 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: 1.230 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.666 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: 0.2021 time to fit residues: 19.4037 Evaluate side-chains 57 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.178501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126533 restraints weight = 6446.299| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.64 r_work: 0.3419 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.675 Fit side-chains REVERT: A 726 ASP cc_start: 0.8243 (p0) cc_final: 0.7821 (t0) REVERT: A 803 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7495 (ttp-110) REVERT: A 851 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6871 (mp) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.1841 time to fit residues: 16.3891 Evaluate side-chains 58 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 34 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.178668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123293 restraints weight = 6408.163| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.97 r_work: 0.3363 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6390 Z= 0.148 Angle : 0.503 6.912 8798 Z= 0.257 Chirality : 0.038 0.136 1020 Planarity : 0.004 0.037 1019 Dihedral : 17.250 108.752 1290 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.99 % Allowed : 13.14 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.32), residues: 686 helix: 1.35 (0.38), residues: 210 sheet: 0.48 (0.40), residues: 172 loop : -1.27 (0.33), residues: 304 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 0.012 0.001 PHE A 699 TYR 0.010 0.001 TYR A 674 ARG 0.005 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 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.680 Fit side-chains REVERT: A 58 ASP cc_start: 0.7901 (t70) cc_final: 0.7631 (t0) REVERT: A 63 LEU cc_start: 0.6045 (tp) cc_final: 0.5821 (tp) REVERT: A 726 ASP cc_start: 0.8332 (p0) cc_final: 0.7911 (t0) REVERT: A 803 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7289 (ttp-110) REVERT: A 851 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6598 (mp) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.1893 time to fit residues: 17.2317 Evaluate side-chains 62 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.178762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123252 restraints weight = 6550.801| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.02 r_work: 0.3351 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6390 Z= 0.143 Angle : 0.487 6.696 8798 Z= 0.247 Chirality : 0.038 0.138 1020 Planarity : 0.004 0.032 1019 Dihedral : 17.146 106.420 1290 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.31 % Allowed : 14.78 % Favored : 83.91 % 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: 0.25 (0.33), residues: 686 helix: 1.60 (0.38), residues: 210 sheet: 0.66 (0.41), residues: 170 loop : -1.16 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 468 HIS 0.002 0.000 HIS A 526 PHE 0.009 0.001 PHE A 699 TYR 0.009 0.001 TYR A 674 ARG 0.004 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 70 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.623 Fit side-chains REVERT: A 58 ASP cc_start: 0.7994 (t70) cc_final: 0.7728 (t0) REVERT: A 726 ASP cc_start: 0.8342 (p0) cc_final: 0.7932 (t0) REVERT: A 769 GLU cc_start: 0.8067 (tt0) cc_final: 0.7409 (pt0) REVERT: A 803 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7105 (ttp-110) REVERT: A 851 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6547 (mp) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.1855 time to fit residues: 16.9015 Evaluate side-chains 63 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.173903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117734 restraints weight = 6428.481| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.99 r_work: 0.3288 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6390 Z= 0.250 Angle : 0.545 6.246 8798 Z= 0.277 Chirality : 0.040 0.147 1020 Planarity : 0.004 0.037 1019 Dihedral : 17.164 104.127 1290 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.97 % Allowed : 15.93 % 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: 0.16 (0.33), residues: 686 helix: 1.45 (0.37), residues: 214 sheet: 0.69 (0.41), residues: 170 loop : -1.25 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 PHE 0.014 0.002 PHE A 481 TYR 0.013 0.002 TYR A 674 ARG 0.004 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 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.710 Fit side-chains REVERT: A 58 ASP cc_start: 0.8012 (t70) cc_final: 0.7749 (t0) REVERT: A 319 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 726 ASP cc_start: 0.8295 (p0) cc_final: 0.7888 (t0) REVERT: A 803 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7108 (ttp-110) REVERT: A 851 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6556 (mp) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.1813 time to fit residues: 16.3298 Evaluate side-chains 63 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 0.0020 chunk 70 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.175336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119221 restraints weight = 6431.989| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.99 r_work: 0.3312 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6390 Z= 0.188 Angle : 0.501 6.164 8798 Z= 0.255 Chirality : 0.038 0.143 1020 Planarity : 0.004 0.036 1019 Dihedral : 17.106 102.096 1290 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.13 % Allowed : 17.08 % Favored : 80.79 % 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 (0.33), residues: 686 helix: 1.60 (0.38), residues: 213 sheet: 0.77 (0.41), residues: 170 loop : -1.19 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 PHE 0.010 0.001 PHE A 782 TYR 0.010 0.001 TYR A 674 ARG 0.004 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 74 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.652 Fit side-chains REVERT: A 58 ASP cc_start: 0.7993 (t70) cc_final: 0.7757 (t0) REVERT: A 319 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 726 ASP cc_start: 0.8284 (p0) cc_final: 0.7879 (t0) REVERT: A 803 ARG cc_start: 0.7302 (ttp80) cc_final: 0.6996 (ttp-110) REVERT: A 851 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6460 (mp) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.1680 time to fit residues: 16.4223 Evaluate side-chains 69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 490 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 786 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 26 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.172282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116319 restraints weight = 6467.479| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.97 r_work: 0.3257 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6390 Z= 0.278 Angle : 0.549 6.298 8798 Z= 0.280 Chirality : 0.040 0.148 1020 Planarity : 0.004 0.038 1019 Dihedral : 17.041 100.157 1290 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.97 % Allowed : 17.08 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.33), residues: 686 helix: 1.42 (0.37), residues: 214 sheet: 0.75 (0.42), residues: 170 loop : -1.28 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 PHE 0.014 0.002 PHE A 481 TYR 0.012 0.002 TYR A 340 ARG 0.005 0.000 ARG A 102 *********************** 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 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.608 Fit side-chains REVERT: A 58 ASP cc_start: 0.8038 (t70) cc_final: 0.7814 (t0) REVERT: A 319 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 657 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6476 (mmt90) REVERT: A 726 ASP cc_start: 0.8265 (p0) cc_final: 0.7849 (t0) REVERT: A 803 ARG cc_start: 0.7326 (ttp80) cc_final: 0.7109 (ttp-110) REVERT: A 851 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6558 (mp) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.2072 time to fit residues: 17.4153 Evaluate side-chains 64 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 490 THR 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 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 66 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119372 restraints weight = 6464.088| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.06 r_work: 0.3311 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2213 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= 0.140 Angle : 0.479 6.471 8798 Z= 0.245 Chirality : 0.037 0.141 1020 Planarity : 0.004 0.033 1019 Dihedral : 16.802 97.494 1290 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.97 % Allowed : 17.08 % Favored : 80.95 % 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: 0.46 (0.34), residues: 686 helix: 1.86 (0.38), residues: 210 sheet: 0.85 (0.42), residues: 170 loop : -1.17 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 468 HIS 0.002 0.001 HIS A 526 PHE 0.007 0.001 PHE A 757 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 794 *********************** 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 73 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.671 Fit side-chains REVERT: A 58 ASP cc_start: 0.8037 (t70) cc_final: 0.7812 (t0) REVERT: A 657 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6854 (mtt90) REVERT: A 726 ASP cc_start: 0.8278 (p0) cc_final: 0.7867 (t0) REVERT: A 803 ARG cc_start: 0.7262 (ttp80) cc_final: 0.7044 (ttp-110) REVERT: A 851 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6381 (mp) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.1830 time to fit residues: 17.2093 Evaluate side-chains 69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 490 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.176202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118693 restraints weight = 6600.478| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.10 r_work: 0.3275 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6390 Z= 0.179 Angle : 0.501 6.865 8798 Z= 0.255 Chirality : 0.038 0.143 1020 Planarity : 0.004 0.034 1019 Dihedral : 16.750 95.671 1290 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 0.46 (0.34), residues: 686 helix: 1.81 (0.38), residues: 211 sheet: 0.88 (0.42), residues: 170 loop : -1.16 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.010 0.001 PHE A 481 TYR 0.009 0.001 TYR A 674 ARG 0.005 0.000 ARG A 794 *********************** 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 to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.804 Fit side-chains REVERT: A 657 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6874 (mtt90) REVERT: A 726 ASP cc_start: 0.8257 (p0) cc_final: 0.7832 (t0) REVERT: A 803 ARG cc_start: 0.7260 (ttp80) cc_final: 0.7038 (ttp-110) REVERT: A 851 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6443 (mp) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.2070 time to fit residues: 18.8719 Evaluate side-chains 64 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 464 PHE Chi-restraints excluded: chain A residue 490 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.173593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115419 restraints weight = 6656.812| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.14 r_work: 0.3243 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6390 Z= 0.260 Angle : 0.554 7.233 8798 Z= 0.281 Chirality : 0.040 0.148 1020 Planarity : 0.004 0.036 1019 Dihedral : 16.763 94.268 1290 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.64 % Allowed : 18.23 % 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: 0.24 (0.33), residues: 686 helix: 1.55 (0.38), residues: 214 sheet: 0.79 (0.42), residues: 170 loop : -1.28 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 PHE 0.013 0.001 PHE A 782 TYR 0.010 0.001 TYR A 674 ARG 0.005 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 62 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.820 Fit side-chains REVERT: A 657 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6504 (mmt90) REVERT: A 726 ASP cc_start: 0.8250 (p0) cc_final: 0.7831 (t0) REVERT: A 803 ARG cc_start: 0.7287 (ttp80) cc_final: 0.7051 (ttp-110) REVERT: A 851 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6460 (mp) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.2387 time to fit residues: 19.2521 Evaluate side-chains 61 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 851 LEU Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.175541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117539 restraints weight = 6656.008| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.13 r_work: 0.3273 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2295 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= 0.192 Angle : 0.516 7.251 8798 Z= 0.263 Chirality : 0.038 0.146 1020 Planarity : 0.004 0.036 1019 Dihedral : 16.682 95.374 1290 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.81 % Allowed : 18.56 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.33), residues: 686 helix: 1.71 (0.38), residues: 211 sheet: 0.84 (0.42), residues: 170 loop : -1.26 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.010 0.001 PHE A 481 TYR 0.009 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: 3285.91 seconds wall clock time: 59 minutes 4.28 seconds (3544.28 seconds total)