Starting phenix.real_space_refine on Thu Nov 14 10:21:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sno_40631/11_2024/8sno_40631.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sno_40631/11_2024/8sno_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sno_40631/11_2024/8sno_40631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sno_40631/11_2024/8sno_40631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sno_40631/11_2024/8sno_40631.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sno_40631/11_2024/8sno_40631.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.43, per 1000 atoms: 0.96 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: 1.64 Conformation dependent library (CDL) restraints added in 726.2 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: 0.61 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: 1.74 Time building geometry restraints manager: 1.79 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 2.510 nonbonded pdb=" O VAL A 477 " pdb="CA CA A 901 " model vdw 2.268 2.510 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.150 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 5828 Z= 0.266 Angle : 0.706 12.070 7907 Z= 0.418 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.32), 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 TRP 0.012 0.001 TRP B 429 HIS 0.006 0.001 HIS B 561 PHE 0.011 0.001 PHE B 668 TYR 0.012 0.001 TYR B 770 ARG 0.003 0.000 ARG B 449 *********************** 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 : 0.723 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: 1.0520 time to fit residues: 91.2237 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 : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5828 Z= 0.241 Angle : 0.563 6.194 7907 Z= 0.294 Chirality : 0.042 0.126 868 Planarity : 0.004 0.042 1015 Dihedral : 4.473 21.034 768 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.74 % Allowed : 7.61 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.32), residues: 714 helix: 1.59 (0.31), residues: 283 sheet: -0.80 (0.83), residues: 41 loop : -0.55 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 429 HIS 0.006 0.001 HIS B 521 PHE 0.015 0.001 PHE B 668 TYR 0.012 0.001 TYR B 340 ARG 0.005 0.001 ARG A 644 *********************** 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 68 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 577 LYS cc_start: 0.7285 (ttpt) cc_final: 0.6935 (tppp) REVERT: B 507 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6404 (mmpt) REVERT: B 728 LEU cc_start: 0.7832 (tp) cc_final: 0.7597 (tp) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.9801 time to fit residues: 68.8784 Evaluate side-chains 51 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 57 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 GLN B 474 ASN B 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5828 Z= 0.159 Angle : 0.483 6.093 7907 Z= 0.252 Chirality : 0.039 0.128 868 Planarity : 0.004 0.039 1015 Dihedral : 4.182 21.071 768 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.74 % Allowed : 9.19 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 714 helix: 1.86 (0.32), residues: 283 sheet: -0.92 (0.76), residues: 46 loop : -0.45 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 429 HIS 0.003 0.001 HIS B 521 PHE 0.014 0.001 PHE B 668 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG A 644 *********************** 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 64 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 577 LYS cc_start: 0.7086 (ttpt) cc_final: 0.6797 (tppp) REVERT: B 507 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6418 (tppt) REVERT: B 728 LEU cc_start: 0.7882 (tp) cc_final: 0.7581 (tp) REVERT: B 819 LYS cc_start: 0.6998 (mtpp) cc_final: 0.6779 (mtpp) outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 0.9279 time to fit residues: 59.4625 Evaluate side-chains 49 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 690 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 68 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 overall best weight: 0.3032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5828 Z= 0.161 Angle : 0.468 6.058 7907 Z= 0.244 Chirality : 0.039 0.127 868 Planarity : 0.003 0.037 1015 Dihedral : 4.047 20.946 768 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.38 % Allowed : 9.67 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 714 helix: 2.02 (0.32), residues: 282 sheet: -0.95 (0.76), residues: 46 loop : -0.42 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 429 HIS 0.003 0.001 HIS B 521 PHE 0.013 0.001 PHE B 668 TYR 0.007 0.001 TYR B 593 ARG 0.003 0.000 ARG A 644 *********************** 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 74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 577 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6839 (tppp) REVERT: B 352 SER cc_start: 0.8521 (p) cc_final: 0.8234 (t) REVERT: B 505 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7090 (ttt) REVERT: B 507 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6355 (tppt) REVERT: B 724 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7684 (m) REVERT: B 728 LEU cc_start: 0.7936 (tp) cc_final: 0.7676 (tp) outliers start: 15 outliers final: 7 residues processed: 71 average time/residue: 0.8972 time to fit residues: 68.1131 Evaluate side-chains 57 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 505 MET Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 689 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5828 Z= 0.236 Angle : 0.517 6.277 7907 Z= 0.270 Chirality : 0.041 0.125 868 Planarity : 0.004 0.039 1015 Dihedral : 4.251 21.379 768 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.69 % Allowed : 10.78 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.32), residues: 714 helix: 1.75 (0.31), residues: 285 sheet: -1.02 (0.76), residues: 46 loop : -0.43 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 662 PHE 0.014 0.001 PHE B 696 TYR 0.010 0.001 TYR B 340 ARG 0.003 0.000 ARG B 449 *********************** 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 70 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 577 LYS cc_start: 0.7357 (ttpt) cc_final: 0.6994 (tppp) REVERT: A 588 LEU cc_start: 0.8468 (mt) cc_final: 0.8229 (mt) REVERT: A 638 ASN cc_start: 0.7692 (m-40) cc_final: 0.7460 (m-40) REVERT: B 408 GLN cc_start: 0.7656 (mt0) cc_final: 0.7209 (mt0) REVERT: B 505 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7508 (ttt) REVERT: B 507 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6334 (tppt) REVERT: B 596 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: B 724 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7694 (m) REVERT: B 728 LEU cc_start: 0.8006 (tp) cc_final: 0.7689 (tp) outliers start: 17 outliers final: 9 residues processed: 67 average time/residue: 0.8786 time to fit residues: 63.4549 Evaluate side-chains 57 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 823 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5828 Z= 0.145 Angle : 0.470 7.935 7907 Z= 0.241 Chirality : 0.038 0.121 868 Planarity : 0.003 0.035 1015 Dihedral : 4.040 21.205 768 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.32), residues: 714 helix: 2.06 (0.32), residues: 282 sheet: -1.10 (0.76), residues: 46 loop : -0.39 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 429 HIS 0.002 0.001 HIS B 521 PHE 0.014 0.001 PHE B 668 TYR 0.006 0.001 TYR B 593 ARG 0.002 0.000 ARG A 644 *********************** 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 69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.666 Fit side-chains REVERT: A 577 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6869 (tppp) REVERT: A 637 MET cc_start: 0.7246 (pmm) cc_final: 0.6834 (mmm) REVERT: B 352 SER cc_start: 0.8604 (p) cc_final: 0.8302 (t) REVERT: B 408 GLN cc_start: 0.7642 (mt0) cc_final: 0.7364 (mt0) REVERT: B 507 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6331 (tppt) REVERT: B 724 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7632 (m) REVERT: B 728 LEU cc_start: 0.7973 (tp) cc_final: 0.7691 (tp) REVERT: B 819 LYS cc_start: 0.6889 (mtpp) cc_final: 0.6601 (ttmm) outliers start: 15 outliers final: 7 residues processed: 65 average time/residue: 0.7884 time to fit residues: 55.4786 Evaluate side-chains 57 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 490 THR Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 732 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 68 optimal weight: 0.0870 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN B 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5828 Z= 0.152 Angle : 0.472 7.075 7907 Z= 0.245 Chirality : 0.038 0.118 868 Planarity : 0.003 0.035 1015 Dihedral : 4.025 20.965 768 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.90 % Allowed : 12.52 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.32), residues: 714 helix: 2.05 (0.32), residues: 283 sheet: -1.14 (0.76), residues: 46 loop : -0.41 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 429 HIS 0.002 0.001 HIS B 662 PHE 0.013 0.001 PHE B 668 TYR 0.006 0.001 TYR B 593 ARG 0.002 0.000 ARG A 644 *********************** 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 63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.754 Fit side-chains REVERT: A 577 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6923 (tppp) REVERT: A 637 MET cc_start: 0.7313 (pmm) cc_final: 0.6815 (mmm) REVERT: B 352 SER cc_start: 0.8605 (p) cc_final: 0.8306 (t) REVERT: B 408 GLN cc_start: 0.7634 (mt0) cc_final: 0.7367 (mt0) REVERT: B 596 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: B 724 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7637 (m) REVERT: B 728 LEU cc_start: 0.8012 (tp) cc_final: 0.7725 (tp) REVERT: B 819 LYS cc_start: 0.6930 (mtpp) cc_final: 0.6652 (ttmm) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.7697 time to fit residues: 49.5613 Evaluate side-chains 55 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 chunk 38 optimal weight: 0.0570 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5828 Z= 0.157 Angle : 0.471 6.743 7907 Z= 0.243 Chirality : 0.039 0.119 868 Planarity : 0.003 0.035 1015 Dihedral : 3.988 20.940 768 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.74 % Allowed : 13.47 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.32), residues: 714 helix: 2.04 (0.32), residues: 283 sheet: -1.14 (0.76), residues: 46 loop : -0.39 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 429 HIS 0.002 0.001 HIS B 662 PHE 0.013 0.001 PHE B 668 TYR 0.008 0.001 TYR A 495 ARG 0.001 0.000 ARG B 449 *********************** 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 60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.696 Fit side-chains REVERT: A 495 TYR cc_start: 0.7503 (m-80) cc_final: 0.7105 (m-80) REVERT: A 577 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6937 (tppp) REVERT: A 637 MET cc_start: 0.7269 (pmm) cc_final: 0.6855 (mmm) REVERT: B 352 SER cc_start: 0.8625 (p) cc_final: 0.8325 (t) REVERT: B 596 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6435 (tm-30) REVERT: B 724 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7619 (m) REVERT: B 728 LEU cc_start: 0.8015 (tp) cc_final: 0.7736 (tp) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.7957 time to fit residues: 49.2173 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 : 0.714 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 70 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5828 Z= 0.169 Angle : 0.485 6.499 7907 Z= 0.250 Chirality : 0.039 0.121 868 Planarity : 0.003 0.035 1015 Dihedral : 4.020 20.961 768 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.74 % Allowed : 13.95 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 714 helix: 2.00 (0.32), residues: 283 sheet: -1.14 (0.76), residues: 46 loop : -0.38 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 429 HIS 0.003 0.001 HIS B 662 PHE 0.013 0.001 PHE B 668 TYR 0.018 0.001 TYR A 495 ARG 0.002 0.000 ARG B 449 *********************** 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 62 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.674 Fit side-chains REVERT: A 577 LYS cc_start: 0.7338 (ttpt) cc_final: 0.7020 (tppp) REVERT: A 637 MET cc_start: 0.7220 (pmm) cc_final: 0.6843 (mmm) REVERT: B 352 SER cc_start: 0.8593 (p) cc_final: 0.8300 (t) REVERT: B 596 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: B 724 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7648 (m) REVERT: B 728 LEU cc_start: 0.8019 (tp) cc_final: 0.7728 (tp) REVERT: B 819 LYS cc_start: 0.6598 (mtpp) cc_final: 0.6305 (tttt) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.8147 time to fit residues: 53.0007 Evaluate side-chains 59 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5828 Z= 0.176 Angle : 0.488 6.389 7907 Z= 0.253 Chirality : 0.039 0.125 868 Planarity : 0.003 0.035 1015 Dihedral : 4.068 20.956 768 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.74 % Allowed : 14.26 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.32), residues: 714 helix: 1.98 (0.32), residues: 283 sheet: -1.10 (0.76), residues: 46 loop : -0.43 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 429 HIS 0.003 0.001 HIS B 662 PHE 0.013 0.001 PHE B 668 TYR 0.010 0.001 TYR A 495 ARG 0.002 0.000 ARG B 449 ********************** 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 63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.696 Fit side-chains REVERT: A 577 LYS cc_start: 0.7388 (ttpt) cc_final: 0.7047 (tppp) REVERT: A 637 MET cc_start: 0.7220 (pmm) cc_final: 0.6890 (mmm) REVERT: B 352 SER cc_start: 0.8597 (p) cc_final: 0.8294 (t) REVERT: B 408 GLN cc_start: 0.7618 (mt0) cc_final: 0.7054 (mt0) REVERT: B 596 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: B 724 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7642 (m) REVERT: B 728 LEU cc_start: 0.8022 (tp) cc_final: 0.7734 (tp) REVERT: B 819 LYS cc_start: 0.6629 (mtpp) cc_final: 0.6331 (tttt) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.7402 time to fit residues: 49.2074 Evaluate side-chains 60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 732 ILE Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3836 r_free = 0.3836 target = 0.156995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114625 restraints weight = 6412.113| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.99 r_work: 0.3227 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5828 Z= 0.252 Angle : 0.540 6.428 7907 Z= 0.280 Chirality : 0.041 0.124 868 Planarity : 0.004 0.036 1015 Dihedral : 4.306 20.885 768 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.90 % Allowed : 14.26 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.32), residues: 714 helix: 1.67 (0.31), residues: 285 sheet: -1.00 (0.76), residues: 46 loop : -0.46 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.006 0.001 HIS B 662 PHE 0.015 0.001 PHE B 696 TYR 0.022 0.002 TYR A 495 ARG 0.004 0.000 ARG B 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2299.09 seconds wall clock time: 41 minutes 55.65 seconds (2515.65 seconds total)