Starting phenix.real_space_refine on Thu Jul 2 02:07:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sno_40631/07_2026/8sno_40631.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sno_40631/07_2026/8sno_40631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sno_40631/07_2026/8sno_40631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sno_40631/07_2026/8sno_40631.map" model { file = "/net/cci-nas-00/data/ceres_data/8sno_40631/07_2026/8sno_40631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sno_40631/07_2026/8sno_40631.cif" } resolution = 2.78 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= 0.052 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 Ca 1 9.91 5 S 55 5.16 5 C 3635 2.51 5 N 961 2.21 5 O 1033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5685 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1745 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3939 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.46, per 1000 atoms: 0.26 Number of scatterers: 5685 At special positions: 0 Unit cell: (72.6264, 85.0059, 134.524, 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) Ca 1 19.99 S 55 16.00 O 1033 8.00 N 961 7.00 C 3635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 573 " distance=2.02 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 611 " distance=2.02 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 603 " distance=2.04 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS B 447 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 579 " - pdb=" SG CYS B 601 " distance=2.04 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: 0.56 Conformation dependent library (CDL) restraints added in 243.7 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 45.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.584A pdb=" N ARG A 584 " --> pdb=" O PRO A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.554A pdb=" N GLN A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 671 through 703 Proline residue: A 686 - end of helix Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 373 through 394 Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 452 through 467 removed outlier: 3.965A pdb=" N ASP B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 487 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 583 through 590 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.931A pdb=" N LYS B 609 " --> pdb=" O HIS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 637 through 659 removed outlier: 3.541A pdb=" N LEU B 652 " --> pdb=" O GLN B 648 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 654 " --> pdb=" O THR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 683 Processing helix chain 'B' and resid 691 through 709 Processing helix chain 'B' and resid 710 through 713 Processing helix chain 'B' and resid 715 through 734 removed outlier: 3.913A pdb=" N ALA B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 756 removed outlier: 3.682A pdb=" N HIS B 744 " --> pdb=" O ASP B 740 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 796 removed outlier: 3.982A pdb=" N TYR B 770 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.965A pdb=" N THR B 808 " --> pdb=" O ILE B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 Processing sheet with id=AA1, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535 removed outlier: 3.514A pdb=" N GLN A 535 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574 Processing sheet with id=AA4, first strand: chain 'A' and resid 590 through 591 removed outlier: 4.330A pdb=" N CYS A 603 " --> pdb=" O CYS A 591 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 633 through 634 Processing sheet with id=AA6, first strand: chain 'B' and resid 403 through 411 Processing sheet with id=AA7, first strand: chain 'B' and resid 481 through 482 Processing sheet with id=AA8, first strand: chain 'B' and resid 527 through 529 removed outlier: 6.556A pdb=" N GLU B 550 " --> pdb=" O GLU B 528 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 579 through 582 238 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.73 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: 1505 1.33 - 1.45: 1108 1.45 - 1.57: 3154 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 5828 Sorted by residual: bond pdb=" CA ALA B 518 " pdb=" C ALA B 518 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.04e-02 9.25e+03 1.14e+01 bond pdb=" CA VAL A 483 " pdb=" C VAL A 483 " ideal model delta sigma weight residual 1.525 1.487 0.037 1.22e-02 6.72e+03 9.31e+00 bond pdb=" N ALA B 518 " pdb=" CA ALA B 518 " ideal model delta sigma weight residual 1.462 1.430 0.032 1.32e-02 5.74e+03 5.96e+00 bond pdb=" C PRO B 503 " pdb=" O PRO B 503 " ideal model delta sigma weight residual 1.240 1.215 0.025 1.12e-02 7.97e+03 5.18e+00 bond pdb=" C VAL B 519 " pdb=" O VAL B 519 " ideal model delta sigma weight residual 1.239 1.212 0.027 1.22e-02 6.72e+03 4.97e+00 ... (remaining 5823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 7775 2.41 - 4.83: 117 4.83 - 7.24: 10 7.24 - 9.66: 3 9.66 - 12.07: 2 Bond angle restraints: 7907 Sorted by residual: angle pdb=" C VAL A 483 " pdb=" CA VAL A 483 " pdb=" CB VAL A 483 " ideal model delta sigma weight residual 111.28 101.24 10.04 1.38e+00 5.25e-01 5.30e+01 angle pdb=" N ALA B 518 " pdb=" CA ALA B 518 " pdb=" C ALA B 518 " ideal model delta sigma weight residual 107.20 95.13 12.07 1.70e+00 3.46e-01 5.04e+01 angle pdb=" N SER B 516 " pdb=" CA SER B 516 " pdb=" C SER B 516 " ideal model delta sigma weight residual 107.99 115.29 -7.30 1.76e+00 3.23e-01 1.72e+01 angle pdb=" N CYS A 567 " pdb=" CA CYS A 567 " pdb=" C CYS A 567 " ideal model delta sigma weight residual 109.31 114.92 -5.61 1.42e+00 4.96e-01 1.56e+01 angle pdb=" C CYS A 567 " pdb=" CA CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sigma weight residual 114.16 105.84 8.32 2.31e+00 1.87e-01 1.30e+01 ... (remaining 7902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 3151 16.25 - 32.50: 271 32.50 - 48.74: 67 48.74 - 64.99: 10 64.99 - 81.24: 6 Dihedral angle restraints: 3505 sinusoidal: 1429 harmonic: 2076 Sorted by residual: dihedral pdb=" CB CYS A 489 " pdb=" SG CYS A 489 " pdb=" SG CYS A 502 " pdb=" CB CYS A 502 " ideal model delta sinusoidal sigma weight residual -86.00 -148.38 62.38 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " pdb=" SG CYS A 611 " pdb=" CB CYS A 611 " ideal model delta sinusoidal sigma weight residual -86.00 -127.79 41.79 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS A 542 " pdb=" SG CYS A 542 " pdb=" SG CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sinusoidal sigma weight residual 93.00 131.38 -38.38 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 3502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 655 0.044 - 0.089: 162 0.089 - 0.133: 46 0.133 - 0.177: 1 0.177 - 0.222: 4 Chirality restraints: 868 Sorted by residual: chirality pdb=" CA SER B 516 " pdb=" N SER B 516 " pdb=" C SER B 516 " pdb=" CB SER B 516 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ALA B 518 " pdb=" N ALA B 518 " pdb=" C ALA B 518 " pdb=" CB ALA B 518 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL A 483 " pdb=" CA VAL A 483 " pdb=" CG1 VAL A 483 " pdb=" CG2 VAL A 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 865 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 517 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C GLY B 517 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY B 517 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA B 518 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 516 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C SER B 516 " -0.049 2.00e-02 2.50e+03 pdb=" O SER B 516 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 517 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 372 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 373 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.020 5.00e-02 4.00e+02 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 114 2.68 - 3.24: 5579 3.24 - 3.79: 8926 3.79 - 4.35: 12282 4.35 - 4.90: 20061 Nonbonded interactions: 46962 Sorted by model distance: nonbonded pdb=" OE2 GLU B 465 " pdb=" OG SER B 602 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR B 376 " pdb=" OE1 GLU B 656 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 480 " pdb="CA CA A 901 " model vdw 2.257 3.250 nonbonded pdb=" O VAL A 477 " pdb="CA CA A 901 " model vdw 2.268 3.250 nonbonded pdb=" NE2 GLN B 522 " pdb=" O PRO B 546 " model vdw 2.322 3.120 ... (remaining 46957 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: 6.780 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.030 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:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5849 Z= 0.240 Angle : 0.712 12.070 7949 Z= 0.420 Chirality : 0.044 0.222 868 Planarity : 0.004 0.036 1015 Dihedral : 12.789 81.238 2102 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.11 (0.32), residues: 714 helix: 1.11 (0.32), residues: 286 sheet: -0.86 (0.84), residues: 45 loop : -0.89 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.012 0.001 TYR B 770 PHE 0.011 0.001 PHE B 668 TRP 0.012 0.001 TRP B 429 HIS 0.006 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.24 ( 5828) covalent geometry : angle 0.70562 / 0.42 ( 7907) SS BOND : bond 0.00383 / 0.26 ( 21) SS BOND : angle 1.49601 / 1.12 ( 42) hydrogen bonds : bond 0.17595 / 11.52 ( 238) hydrogen bonds : angle 6.12331 / 4.23 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.215 Fit side-chains REVERT: B 408 GLN cc_start: 0.7540 (mt0) cc_final: 0.7202 (mt0) REVERT: B 455 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6421 (tp30) REVERT: B 459 LEU cc_start: 0.8318 (mp) cc_final: 0.7925 (mp) REVERT: B 728 LEU cc_start: 0.7612 (tp) cc_final: 0.7393 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.4798 time to fit residues: 41.3679 Evaluate side-chains 54 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120625 restraints weight = 6480.084| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.87 r_work: 0.3337 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5849 Z= 0.134 Angle : 0.550 7.107 7949 Z= 0.286 Chirality : 0.041 0.124 868 Planarity : 0.004 0.040 1015 Dihedral : 4.371 20.746 768 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.74 % Allowed : 7.45 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.50 (0.32), residues: 714 helix: 1.71 (0.32), residues: 282 sheet: -0.84 (0.83), residues: 41 loop : -0.55 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.010 0.001 TYR B 340 PHE 0.015 0.001 PHE B 668 TRP 0.012 0.001 TRP B 429 HIS 0.005 0.001 HIS B 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 5828) covalent geometry : angle 0.54464 / 0.28 ( 7907) SS BOND : bond 0.00426 / 0.23 ( 21) SS BOND : angle 1.22445 / 0.88 ( 42) hydrogen bonds : bond 0.04325 / 2.91 ( 238) hydrogen bonds : angle 4.57905 / 3.15 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 494 MET cc_start: 0.8213 (ttp) cc_final: 0.7959 (ttp) REVERT: A 577 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6781 (tppp) REVERT: B 507 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6433 (mmpt) REVERT: B 728 LEU cc_start: 0.7810 (tp) cc_final: 0.7529 (tp) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.3642 time to fit residues: 26.2440 Evaluate side-chains 50 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 551 GLN B 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115874 restraints weight = 6338.581| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.90 r_work: 0.3245 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5849 Z= 0.153 Angle : 0.537 6.129 7949 Z= 0.281 Chirality : 0.041 0.127 868 Planarity : 0.004 0.041 1015 Dihedral : 4.347 21.574 768 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.06 % Allowed : 9.19 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.32), residues: 714 helix: 1.64 (0.31), residues: 283 sheet: -0.82 (0.82), residues: 41 loop : -0.52 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 644 TYR 0.011 0.001 TYR B 593 PHE 0.014 0.001 PHE B 696 TRP 0.012 0.001 TRP B 629 HIS 0.006 0.001 HIS B 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 5828) covalent geometry : angle 0.53329 / 0.28 ( 7907) SS BOND : bond 0.00262 / 0.17 ( 21) SS BOND : angle 1.05728 / 0.82 ( 42) hydrogen bonds : bond 0.04516 / 3.00 ( 238) hydrogen bonds : angle 4.43883 / 3.05 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 577 LYS cc_start: 0.7157 (ttpt) cc_final: 0.6701 (tppp) REVERT: B 507 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6471 (tppt) REVERT: B 724 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.7887 (m) REVERT: B 728 LEU cc_start: 0.7984 (tp) cc_final: 0.7696 (tp) REVERT: B 819 LYS cc_start: 0.7003 (mtpp) cc_final: 0.6742 (mtpp) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.3478 time to fit residues: 22.0592 Evaluate side-chains 53 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 823 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115654 restraints weight = 6382.040| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.87 r_work: 0.3257 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5849 Z= 0.162 Angle : 0.537 6.281 7949 Z= 0.281 Chirality : 0.041 0.130 868 Planarity : 0.004 0.041 1015 Dihedral : 4.421 21.907 768 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.22 % Allowed : 10.78 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.38 (0.31), residues: 714 helix: 1.53 (0.31), residues: 286 sheet: -1.08 (0.73), residues: 50 loop : -0.53 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 449 TYR 0.011 0.001 TYR B 340 PHE 0.014 0.001 PHE B 696 TRP 0.012 0.001 TRP B 629 HIS 0.005 0.001 HIS B 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 5828) covalent geometry : angle 0.53388 / 0.28 ( 7907) SS BOND : bond 0.00275 / 0.18 ( 21) SS BOND : angle 0.96459 / 0.73 ( 42) hydrogen bonds : bond 0.04503 / 2.98 ( 238) hydrogen bonds : angle 4.38411 / 3.02 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 577 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6909 (tppp) REVERT: A 612 VAL cc_start: 0.8644 (t) cc_final: 0.8412 (p) REVERT: B 408 GLN cc_start: 0.7719 (mt0) cc_final: 0.7266 (mt0) REVERT: B 505 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7567 (ttt) REVERT: B 507 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6503 (tppt) REVERT: B 565 GLU cc_start: 0.7686 (mp0) cc_final: 0.7457 (mt-10) REVERT: B 724 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7927 (m) REVERT: B 728 LEU cc_start: 0.8065 (tp) cc_final: 0.7749 (tp) REVERT: B 819 LYS cc_start: 0.6992 (mtpp) cc_final: 0.6745 (mtpp) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 0.3663 time to fit residues: 24.6452 Evaluate side-chains 55 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 724 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118492 restraints weight = 6587.000| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.83 r_work: 0.3281 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5849 Z= 0.138 Angle : 0.511 6.851 7949 Z= 0.266 Chirality : 0.040 0.127 868 Planarity : 0.004 0.040 1015 Dihedral : 4.362 22.021 768 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.85 % Allowed : 11.09 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.47 (0.32), residues: 714 helix: 1.62 (0.31), residues: 285 sheet: -1.13 (0.73), residues: 50 loop : -0.47 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 449 TYR 0.017 0.001 TYR A 495 PHE 0.013 0.001 PHE B 668 TRP 0.012 0.001 TRP B 429 HIS 0.004 0.001 HIS B 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5828) covalent geometry : angle 0.50862 / 0.27 ( 7907) SS BOND : bond 0.00234 / 0.15 ( 21) SS BOND : angle 0.83835 / 0.64 ( 42) hydrogen bonds : bond 0.04195 / 2.77 ( 238) hydrogen bonds : angle 4.27783 / 2.93 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 494 MET cc_start: 0.8432 (ttp) cc_final: 0.8186 (ttp) REVERT: A 495 TYR cc_start: 0.7681 (m-80) cc_final: 0.7391 (m-80) REVERT: A 577 LYS cc_start: 0.7328 (ttpt) cc_final: 0.6861 (tppp) REVERT: A 588 LEU cc_start: 0.8226 (mt) cc_final: 0.7998 (mt) REVERT: A 612 VAL cc_start: 0.8643 (t) cc_final: 0.8427 (p) REVERT: A 637 MET cc_start: 0.7979 (pmm) cc_final: 0.6807 (mmm) REVERT: B 352 SER cc_start: 0.8690 (p) cc_final: 0.8357 (t) REVERT: B 505 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7638 (ttt) REVERT: B 507 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6366 (tppt) REVERT: B 565 GLU cc_start: 0.7718 (mp0) cc_final: 0.7430 (mt-10) REVERT: B 724 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7921 (m) REVERT: B 819 LYS cc_start: 0.6920 (mtpp) cc_final: 0.6680 (mtpp) outliers start: 18 outliers final: 7 residues processed: 67 average time/residue: 0.3184 time to fit residues: 22.9183 Evaluate side-chains 58 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 724 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 70 optimal weight: 0.0030 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 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 = 0.3894 r_free = 0.3894 target = 0.160479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118721 restraints weight = 6427.461| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.92 r_work: 0.3302 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5849 Z= 0.113 Angle : 0.486 5.999 7949 Z= 0.253 Chirality : 0.039 0.128 868 Planarity : 0.003 0.038 1015 Dihedral : 4.249 21.826 768 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.38 % Allowed : 12.36 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.57 (0.32), residues: 714 helix: 1.77 (0.31), residues: 285 sheet: -1.16 (0.73), residues: 50 loop : -0.45 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 449 TYR 0.010 0.001 TYR A 495 PHE 0.013 0.001 PHE B 668 TRP 0.012 0.001 TRP B 429 HIS 0.003 0.001 HIS B 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5828) covalent geometry : angle 0.48405 / 0.25 ( 7907) SS BOND : bond 0.00193 / 0.12 ( 21) SS BOND : angle 0.74394 / 0.59 ( 42) hydrogen bonds : bond 0.03776 / 2.50 ( 238) hydrogen bonds : angle 4.16635 / 2.85 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.131 Fit side-chains REVERT: A 494 MET cc_start: 0.8424 (ttp) cc_final: 0.8175 (ttp) REVERT: A 495 TYR cc_start: 0.7734 (m-80) cc_final: 0.7377 (m-80) REVERT: A 577 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6777 (tppp) REVERT: A 637 MET cc_start: 0.7887 (pmm) cc_final: 0.6833 (mmm) REVERT: B 352 SER cc_start: 0.8718 (p) cc_final: 0.8382 (t) REVERT: B 408 GLN cc_start: 0.7680 (mt0) cc_final: 0.7230 (mt0) REVERT: B 505 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: B 506 ASP cc_start: 0.7200 (t0) cc_final: 0.6991 (p0) REVERT: B 507 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6345 (tppt) REVERT: B 565 GLU cc_start: 0.7669 (mp0) cc_final: 0.7377 (mt-10) REVERT: B 596 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: B 819 LYS cc_start: 0.6840 (mtpp) cc_final: 0.6631 (mtpp) outliers start: 15 outliers final: 8 residues processed: 66 average time/residue: 0.2792 time to fit residues: 19.8567 Evaluate side-chains 61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 823 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 0.0970 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115802 restraints weight = 6468.108| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.00 r_work: 0.3235 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5849 Z= 0.133 Angle : 0.500 5.398 7949 Z= 0.261 Chirality : 0.040 0.120 868 Planarity : 0.004 0.039 1015 Dihedral : 4.275 21.676 768 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.85 % Allowed : 12.20 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.50 (0.32), residues: 714 helix: 1.70 (0.31), residues: 285 sheet: -1.18 (0.73), residues: 50 loop : -0.50 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.009 0.001 TYR B 593 PHE 0.013 0.001 PHE B 668 TRP 0.012 0.001 TRP B 629 HIS 0.004 0.001 HIS B 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 5828) covalent geometry : angle 0.49840 / 0.26 ( 7907) SS BOND : bond 0.00227 / 0.14 ( 21) SS BOND : angle 0.79160 / 0.62 ( 42) hydrogen bonds : bond 0.04020 / 2.65 ( 238) hydrogen bonds : angle 4.20206 / 2.88 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.215 Fit side-chains REVERT: A 494 MET cc_start: 0.8520 (ttp) cc_final: 0.8260 (ttp) REVERT: A 495 TYR cc_start: 0.7810 (m-80) cc_final: 0.7392 (m-80) REVERT: A 577 LYS cc_start: 0.7221 (ttpt) cc_final: 0.6691 (tppp) REVERT: B 352 SER cc_start: 0.8702 (p) cc_final: 0.8328 (t) REVERT: B 408 GLN cc_start: 0.7654 (mt0) cc_final: 0.7168 (mt0) REVERT: B 505 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7731 (ttt) REVERT: B 506 ASP cc_start: 0.7290 (t0) cc_final: 0.6815 (p0) REVERT: B 507 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6330 (tppt) REVERT: B 565 GLU cc_start: 0.7643 (mp0) cc_final: 0.7303 (mt-10) REVERT: B 596 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: B 724 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.7862 (m) REVERT: B 728 LEU cc_start: 0.8091 (tp) cc_final: 0.7883 (tp) outliers start: 18 outliers final: 10 residues processed: 64 average time/residue: 0.3038 time to fit residues: 20.8515 Evaluate side-chains 60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 70 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0000 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 ASN B 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120153 restraints weight = 6443.609| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.01 r_work: 0.3297 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5849 Z= 0.093 Angle : 0.463 7.628 7949 Z= 0.240 Chirality : 0.038 0.117 868 Planarity : 0.003 0.036 1015 Dihedral : 4.021 21.383 768 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.69 % Allowed : 13.63 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.32), residues: 714 helix: 2.00 (0.32), residues: 285 sheet: -1.27 (0.73), residues: 50 loop : -0.47 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 644 TYR 0.009 0.001 TYR A 495 PHE 0.014 0.001 PHE B 668 TRP 0.013 0.001 TRP B 429 HIS 0.002 0.001 HIS B 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 5828) covalent geometry : angle 0.46184 / 0.24 ( 7907) SS BOND : bond 0.00114 / 0.07 ( 21) SS BOND : angle 0.60323 / 0.48 ( 42) hydrogen bonds : bond 0.03252 / 2.16 ( 238) hydrogen bonds : angle 4.02781 / 2.75 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.144 Fit side-chains REVERT: A 494 MET cc_start: 0.8524 (ttp) cc_final: 0.8296 (ttp) REVERT: A 495 TYR cc_start: 0.7783 (m-80) cc_final: 0.7382 (m-80) REVERT: A 577 LYS cc_start: 0.7097 (ttpt) cc_final: 0.6597 (tppp) REVERT: A 583 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 637 MET cc_start: 0.7824 (pmm) cc_final: 0.6881 (mmm) REVERT: B 352 SER cc_start: 0.8720 (p) cc_final: 0.8353 (t) REVERT: B 506 ASP cc_start: 0.7313 (t0) cc_final: 0.6877 (p0) REVERT: B 507 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6372 (tppt) REVERT: B 596 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: B 819 LYS cc_start: 0.6522 (mtpp) cc_final: 0.6261 (ttpt) outliers start: 17 outliers final: 10 residues processed: 66 average time/residue: 0.3541 time to fit residues: 25.1348 Evaluate side-chains 61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113904 restraints weight = 6488.974| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.99 r_work: 0.3220 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5849 Z= 0.176 Angle : 0.560 7.722 7949 Z= 0.289 Chirality : 0.042 0.167 868 Planarity : 0.004 0.040 1015 Dihedral : 4.361 21.168 768 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.54 % Allowed : 14.26 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.43 (0.32), residues: 714 helix: 1.63 (0.31), residues: 285 sheet: -1.17 (0.72), residues: 50 loop : -0.54 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 449 TYR 0.012 0.002 TYR B 593 PHE 0.016 0.001 PHE B 696 TRP 0.012 0.001 TRP B 629 HIS 0.006 0.001 HIS B 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 5828) covalent geometry : angle 0.55774 / 0.29 ( 7907) SS BOND : bond 0.00279 / 0.17 ( 21) SS BOND : angle 0.89625 / 0.69 ( 42) hydrogen bonds : bond 0.04487 / 2.94 ( 238) hydrogen bonds : angle 4.29410 / 2.94 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.163 Fit side-chains REVERT: A 494 MET cc_start: 0.8478 (ttp) cc_final: 0.8271 (ttp) REVERT: A 495 TYR cc_start: 0.7832 (m-80) cc_final: 0.7425 (m-80) REVERT: A 577 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6798 (tppp) REVERT: A 583 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 637 MET cc_start: 0.7858 (pmm) cc_final: 0.6974 (mmm) REVERT: B 352 SER cc_start: 0.8708 (p) cc_final: 0.8361 (t) REVERT: B 408 GLN cc_start: 0.7748 (mt0) cc_final: 0.7113 (mt0) REVERT: B 505 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8001 (ttt) REVERT: B 506 ASP cc_start: 0.7291 (t0) cc_final: 0.6820 (p0) REVERT: B 507 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6357 (tppt) REVERT: B 565 GLU cc_start: 0.7814 (mp0) cc_final: 0.7524 (mt-10) REVERT: B 596 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: B 724 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7888 (m) REVERT: B 728 LEU cc_start: 0.8168 (tp) cc_final: 0.7961 (tp) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.3420 time to fit residues: 22.5879 Evaluate side-chains 59 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 724 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 61 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 31 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.0170 chunk 56 optimal weight: 0.6980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** 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 = 0.3865 r_free = 0.3865 target = 0.159670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115886 restraints weight = 6501.730| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.00 r_work: 0.3259 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5849 Z= 0.106 Angle : 0.487 7.464 7949 Z= 0.252 Chirality : 0.039 0.124 868 Planarity : 0.003 0.037 1015 Dihedral : 4.158 21.580 768 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.69 % Allowed : 14.42 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.61 (0.32), residues: 714 helix: 1.86 (0.31), residues: 285 sheet: -1.19 (0.72), residues: 50 loop : -0.50 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 338 TYR 0.008 0.001 TYR A 495 PHE 0.014 0.001 PHE B 668 TRP 0.013 0.001 TRP B 429 HIS 0.004 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 5828) covalent geometry : angle 0.48618 / 0.25 ( 7907) SS BOND : bond 0.00178 / 0.11 ( 21) SS BOND : angle 0.68357 / 0.54 ( 42) hydrogen bonds : bond 0.03601 / 2.37 ( 238) hydrogen bonds : angle 4.11722 / 2.81 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.235 Fit side-chains REVERT: A 495 TYR cc_start: 0.7830 (m-80) cc_final: 0.7444 (m-80) REVERT: A 577 LYS cc_start: 0.7178 (ttpt) cc_final: 0.6651 (tppp) REVERT: A 583 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 637 MET cc_start: 0.7802 (pmm) cc_final: 0.6997 (mmm) REVERT: B 352 SER cc_start: 0.8725 (p) cc_final: 0.8355 (t) REVERT: B 408 GLN cc_start: 0.7653 (mt0) cc_final: 0.7050 (mt0) REVERT: B 506 ASP cc_start: 0.7281 (t0) cc_final: 0.6781 (p0) REVERT: B 507 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6395 (tppt) REVERT: B 565 GLU cc_start: 0.7655 (mp0) cc_final: 0.7342 (mt-10) REVERT: B 580 GLU cc_start: 0.8495 (pt0) cc_final: 0.8168 (pp20) REVERT: B 596 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: B 724 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7841 (m) REVERT: B 819 LYS cc_start: 0.6447 (mtpp) cc_final: 0.6126 (tttm) outliers start: 17 outliers final: 9 residues processed: 64 average time/residue: 0.3469 time to fit residues: 23.9045 Evaluate side-chains 63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 724 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 25 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 551 GLN B 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114929 restraints weight = 6382.585| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.98 r_work: 0.3245 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5849 Z= 0.123 Angle : 0.511 7.384 7949 Z= 0.262 Chirality : 0.040 0.138 868 Planarity : 0.004 0.038 1015 Dihedral : 4.174 21.305 768 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.06 % Allowed : 15.37 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.32), residues: 714 helix: 1.84 (0.31), residues: 285 sheet: -1.16 (0.72), residues: 50 loop : -0.50 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 449 TYR 0.018 0.001 TYR A 495 PHE 0.013 0.001 PHE B 668 TRP 0.012 0.001 TRP B 429 HIS 0.004 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 5828) covalent geometry : angle 0.50947 / 0.26 ( 7907) SS BOND : bond 0.00190 / 0.12 ( 21) SS BOND : angle 0.74146 / 0.58 ( 42) hydrogen bonds : bond 0.03802 / 2.50 ( 238) hydrogen bonds : angle 4.13679 / 2.83 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1955.13 seconds wall clock time: 34 minutes 3.64 seconds (2043.64 seconds total)