Starting phenix.real_space_refine on Tue Aug 4 19:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e29_27829/08_2026/8e29_27829.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'RNAv2': 33} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 27} Time building chain proxies: 1.09, per 1000 atoms: 0.18 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: 0.43 Conformation dependent library (CDL) restraints added in 215.8 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: 0.40 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: 0.75 Time building geometry restraints manager: 0.52 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: 8026 1.87 - 3.75: 614 3.75 - 5.62: 126 5.62 - 7.50: 22 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 - 15.57: 3248 15.57 - 31.13: 396 31.13 - 46.70: 132 46.70 - 62.27: 61 62.27 - 77.84: 16 Dihedral angle restraints: 3853 sinusoidal: 1823 harmonic: 2030 Sorted by residual: dihedral pdb=" C4' U B 11 " pdb=" C3' U B 11 " pdb=" C2' U B 11 " pdb=" C1' U B 11 " ideal model delta sinusoidal sigma weight residual 36.35 -41.49 77.84 1 3.10e+00 1.04e-01 7.88e+02 dihedral pdb=" C4' U B 24 " pdb=" C3' U B 24 " pdb=" C2' U B 24 " pdb=" C1' U B 24 " ideal model delta sinusoidal sigma weight residual 36.34 -37.61 73.95 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' C B 12 " pdb=" C3' C B 12 " pdb=" C2' C B 12 " pdb=" C1' C B 12 " ideal model delta sinusoidal sigma weight residual 36.34 -35.40 71.75 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 3850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 725 0.074 - 0.147: 202 0.147 - 0.221: 58 0.221 - 0.295: 30 0.295 - 0.369: 5 Chirality restraints: 1020 Sorted by residual: chirality pdb=" P C B 12 " pdb=" OP1 C B 12 " pdb=" OP2 C B 12 " pdb=" O5' C B 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3' U B 11 " pdb=" C4' U B 11 " pdb=" O3' U B 11 " pdb=" C2' U B 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.33e+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: 1.610 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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= 0.499 Angle : 1.188 9.374 8798 Z= 0.631 Chirality : 0.086 0.369 1020 Planarity : 0.008 0.058 1019 Dihedral : 16.847 77.836 2531 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG A 104 TYR 0.028 0.005 TYR A 853 PHE 0.049 0.004 PHE A 699 TRP 0.024 0.005 TRP A 468 HIS 0.017 0.002 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.01233 / 0.50 ( 6390) covalent geometry : angle 1.18769 / 0.63 ( 8798) hydrogen bonds : bond 0.16817 / 11.17 ( 258) hydrogen bonds : angle 6.09197 / 4.09 ( 715) *********************** 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 : 0.220 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: 0.0613 time to fit residues: 6.0623 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 : 0.121 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4159 r_free = 0.4159 target = 0.179262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126889 restraints weight = 6461.882| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.65 r_work: 0.3447 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6390 Z= 0.147 Angle : 0.862 13.372 8798 Z= 0.370 Chirality : 0.068 0.697 1020 Planarity : 0.005 0.042 1019 Dihedral : 13.872 149.941 1151 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.82 % Allowed : 11.17 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.31), residues: 686 helix: 0.61 (0.36), residues: 214 sheet: 0.36 (0.40), residues: 168 loop : -1.51 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 803 TYR 0.012 0.001 TYR A 653 PHE 0.014 0.001 PHE A 699 TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 6390) covalent geometry : angle 0.86222 / 0.37 ( 8798) hydrogen bonds : bond 0.05527 / 3.58 ( 258) hydrogen bonds : angle 4.62654 / 3.21 ( 715) *********************** 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 68 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.124 Fit side-chains REVERT: A 58 ASP cc_start: 0.8041 (t70) cc_final: 0.7774 (t0) REVERT: A 726 ASP cc_start: 0.8197 (p0) cc_final: 0.7775 (t0) REVERT: A 803 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7569 (ttp-110) REVERT: A 851 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6948 (mp) outliers start: 5 outliers final: 1 residues processed: 67 average time/residue: 0.0516 time to fit residues: 4.6923 Evaluate side-chains 59 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.173398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117023 restraints weight = 6363.607| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.97 r_work: 0.3282 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1627 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= 0.185 Angle : 0.748 8.642 8798 Z= 0.338 Chirality : 0.056 0.458 1020 Planarity : 0.005 0.042 1019 Dihedral : 13.896 154.570 1146 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.31 % Allowed : 13.79 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.32), residues: 686 helix: 0.89 (0.37), residues: 213 sheet: 0.49 (0.40), residues: 172 loop : -1.52 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.012 0.002 TYR A 674 PHE 0.018 0.002 PHE A 699 TRP 0.016 0.002 TRP A 468 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 ( 6390) covalent geometry : angle 0.74801 / 0.34 ( 8798) hydrogen bonds : bond 0.05953 / 3.84 ( 258) hydrogen bonds : angle 4.50810 / 3.14 ( 715) *********************** 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 63 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.207 Fit side-chains REVERT: A 726 ASP cc_start: 0.8312 (p0) cc_final: 0.7900 (t0) REVERT: A 803 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7384 (ttp-110) REVERT: A 851 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6616 (mp) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.0632 time to fit residues: 5.4073 Evaluate side-chains 58 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.176896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118276 restraints weight = 6546.260| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.13 r_work: 0.3268 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6390 Z= 0.132 Angle : 0.673 7.403 8798 Z= 0.299 Chirality : 0.053 0.346 1020 Planarity : 0.004 0.037 1019 Dihedral : 13.604 155.534 1146 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.31 % Allowed : 16.26 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.32), residues: 686 helix: 1.29 (0.37), residues: 212 sheet: 0.58 (0.40), residues: 172 loop : -1.42 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.010 0.001 TYR A 674 PHE 0.012 0.001 PHE A 699 TRP 0.015 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6390) covalent geometry : angle 0.67326 / 0.30 ( 8798) hydrogen bonds : bond 0.04861 / 3.15 ( 258) hydrogen bonds : angle 4.25058 / 2.98 ( 715) *********************** 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 68 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.201 Fit side-chains REVERT: A 58 ASP cc_start: 0.8019 (t70) cc_final: 0.7784 (t0) REVERT: A 726 ASP cc_start: 0.8310 (p0) cc_final: 0.7892 (t0) REVERT: A 803 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7228 (ttp-110) REVERT: A 851 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6554 (mp) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.0507 time to fit residues: 4.8688 Evaluate side-chains 64 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 19 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122027 restraints weight = 6616.932| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.13 r_work: 0.3323 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2266 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= 0.099 Angle : 0.623 7.280 8798 Z= 0.274 Chirality : 0.050 0.327 1020 Planarity : 0.004 0.036 1019 Dihedral : 13.389 158.180 1146 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.13 % Allowed : 16.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.33), residues: 686 helix: 1.69 (0.38), residues: 209 sheet: 0.74 (0.41), residues: 170 loop : -1.19 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.008 0.001 TYR A 674 PHE 0.009 0.001 PHE A 699 TRP 0.014 0.001 TRP A 468 HIS 0.007 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 6390) covalent geometry : angle 0.62328 / 0.27 ( 8798) hydrogen bonds : bond 0.03811 / 2.47 ( 258) hydrogen bonds : angle 4.01851 / 2.83 ( 715) *********************** 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 80 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.241 Fit side-chains REVERT: A 58 ASP cc_start: 0.8012 (t70) cc_final: 0.7750 (t0) REVERT: A 726 ASP cc_start: 0.8249 (p0) cc_final: 0.7851 (t0) REVERT: A 803 ARG cc_start: 0.7306 (ttp80) cc_final: 0.6992 (ttp-110) outliers start: 13 outliers final: 6 residues processed: 76 average time/residue: 0.0515 time to fit residues: 5.6733 Evaluate side-chains 65 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 762 VAL 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 8 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.176495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118107 restraints weight = 6525.988| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.11 r_work: 0.3265 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2202 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= 0.141 Angle : 0.666 7.269 8798 Z= 0.298 Chirality : 0.051 0.328 1020 Planarity : 0.004 0.035 1019 Dihedral : 13.225 159.413 1144 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.30 % Allowed : 17.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.33), residues: 686 helix: 1.64 (0.38), residues: 211 sheet: 0.83 (0.41), residues: 170 loop : -1.20 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.010 0.001 TYR A 674 PHE 0.012 0.001 PHE A 481 TRP 0.011 0.001 TRP A 468 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 6390) covalent geometry : angle 0.66626 / 0.30 ( 8798) hydrogen bonds : bond 0.04741 / 3.04 ( 258) hydrogen bonds : angle 4.12289 / 2.89 ( 715) *********************** 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 to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.186 Fit side-chains REVERT: A 58 ASP cc_start: 0.8041 (t70) cc_final: 0.7820 (t0) REVERT: A 657 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6809 (mtt90) REVERT: A 726 ASP cc_start: 0.8265 (p0) cc_final: 0.7850 (t0) REVERT: A 803 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7119 (ttp-110) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 0.0526 time to fit residues: 5.0666 Evaluate side-chains 68 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4096 r_free = 0.4096 target = 0.178293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120289 restraints weight = 6521.200| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.11 r_work: 0.3294 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2370 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= 0.111 Angle : 0.632 7.300 8798 Z= 0.280 Chirality : 0.050 0.316 1020 Planarity : 0.004 0.035 1019 Dihedral : 13.127 160.687 1144 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.81 % Allowed : 18.39 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.33), residues: 686 helix: 1.82 (0.38), residues: 209 sheet: 0.84 (0.42), residues: 170 loop : -1.19 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.009 0.001 TYR A 674 PHE 0.009 0.001 PHE A 481 TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6390) covalent geometry : angle 0.63205 / 0.28 ( 8798) hydrogen bonds : bond 0.04183 / 2.69 ( 258) hydrogen bonds : angle 4.03902 / 2.83 ( 715) *********************** 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 71 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.129 Fit side-chains REVERT: A 657 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6391 (mmt90) REVERT: A 726 ASP cc_start: 0.8243 (p0) cc_final: 0.7812 (t0) REVERT: A 803 ARG cc_start: 0.7284 (ttp80) cc_final: 0.7063 (ttp-110) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.0486 time to fit residues: 4.5534 Evaluate side-chains 66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 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 15 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 39 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4244 r_free = 0.4244 target = 0.186576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135655 restraints weight = 6699.923| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.68 r_work: 0.3459 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6390 Z= 0.098 Angle : 0.619 7.305 8798 Z= 0.274 Chirality : 0.050 0.308 1020 Planarity : 0.004 0.035 1019 Dihedral : 12.976 161.780 1144 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.97 % Allowed : 18.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.33), residues: 686 helix: 1.79 (0.38), residues: 215 sheet: 0.92 (0.42), residues: 170 loop : -1.15 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.007 0.001 TYR A 674 PHE 0.008 0.001 PHE A 481 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6390) covalent geometry : angle 0.61901 / 0.27 ( 8798) hydrogen bonds : bond 0.03632 / 2.33 ( 258) hydrogen bonds : angle 3.91278 / 2.75 ( 715) *********************** 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 70 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.223 Fit side-chains REVERT: A 657 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6606 (mmt90) REVERT: A 726 ASP cc_start: 0.8176 (p0) cc_final: 0.7748 (t0) REVERT: A 803 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7176 (ttp-110) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.0632 time to fit residues: 5.8563 Evaluate side-chains 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 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 6 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4222 r_free = 0.4222 target = 0.184243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132700 restraints weight = 6704.320| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.71 r_work: 0.3457 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2599 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= 0.105 Angle : 0.623 7.292 8798 Z= 0.276 Chirality : 0.050 0.303 1020 Planarity : 0.004 0.034 1019 Dihedral : 12.927 162.708 1144 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 : 1.97 % Allowed : 18.72 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.33), residues: 686 helix: 1.77 (0.38), residues: 215 sheet: 0.93 (0.42), residues: 170 loop : -1.16 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.008 0.001 TYR A 340 PHE 0.009 0.001 PHE A 481 TRP 0.011 0.001 TRP A 468 HIS 0.003 0.000 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6390) covalent geometry : angle 0.62300 / 0.28 ( 8798) hydrogen bonds : bond 0.03878 / 2.49 ( 258) hydrogen bonds : angle 3.91385 / 2.75 ( 715) *********************** 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 70 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.146 Fit side-chains REVERT: A 657 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6612 (mmt90) REVERT: A 726 ASP cc_start: 0.8190 (p0) cc_final: 0.7749 (t0) REVERT: A 803 ARG cc_start: 0.7398 (ttp80) cc_final: 0.7169 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.0720 time to fit residues: 6.5237 Evaluate side-chains 65 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4249 r_free = 0.4249 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136132 restraints weight = 6628.790| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.68 r_work: 0.3496 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6390 Z= 0.096 Angle : 0.612 7.373 8798 Z= 0.270 Chirality : 0.049 0.296 1020 Planarity : 0.004 0.033 1019 Dihedral : 12.840 163.496 1144 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.31 % Allowed : 18.88 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.34), residues: 686 helix: 2.05 (0.38), residues: 209 sheet: 0.99 (0.42), residues: 170 loop : -1.06 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.007 0.001 TYR A 674 PHE 0.008 0.001 PHE A 481 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6390) covalent geometry : angle 0.61229 / 0.27 ( 8798) hydrogen bonds : bond 0.03533 / 2.27 ( 258) hydrogen bonds : angle 3.85868 / 2.71 ( 715) ********************** 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 66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.218 Fit side-chains REVERT: A 657 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6568 (mmt90) REVERT: A 726 ASP cc_start: 0.8184 (p0) cc_final: 0.7723 (t0) REVERT: A 803 ARG cc_start: 0.7374 (ttp80) cc_final: 0.7149 (ttp-110) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.0730 time to fit residues: 6.4642 Evaluate side-chains 65 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU 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 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4227 r_free = 0.4227 target = 0.184830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133301 restraints weight = 6588.522| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.71 r_work: 0.3465 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2745 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= 0.105 Angle : 0.619 7.240 8798 Z= 0.274 Chirality : 0.049 0.292 1020 Planarity : 0.004 0.033 1019 Dihedral : 12.797 164.252 1144 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.81 % Allowed : 18.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.34), residues: 686 helix: 2.07 (0.38), residues: 210 sheet: 1.02 (0.42), residues: 170 loop : -1.05 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.008 0.001 TYR A 674 PHE 0.009 0.001 PHE A 481 TRP 0.010 0.001 TRP A 468 HIS 0.003 0.000 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 6390) covalent geometry : angle 0.61929 / 0.27 ( 8798) hydrogen bonds : bond 0.03829 / 2.46 ( 258) hydrogen bonds : angle 3.86037 / 2.71 ( 715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.27 seconds wall clock time: 23 minutes 6.61 seconds (1386.61 seconds total)