Starting phenix.real_space_refine on Tue Jan 14 18:39:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r35_18861/01_2025/8r35_18861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r35_18861/01_2025/8r35_18861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r35_18861/01_2025/8r35_18861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r35_18861/01_2025/8r35_18861.map" model { file = "/net/cci-nas-00/data/ceres_data/8r35_18861/01_2025/8r35_18861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r35_18861/01_2025/8r35_18861.cif" } resolution = 3.12 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= 0.005 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4755 2.51 5 N 1112 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3530 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain: "B" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 1 Time building chain proxies: 5.78, per 1000 atoms: 0.81 Number of scatterers: 7150 At special positions: 0 Unit cell: (83.085, 86.523, 100.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1231 8.00 N 1112 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 Processing helix chain 'A' and resid 458 through 474 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.508A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.663A pdb=" N MET A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.631A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 567 removed outlier: 3.622A pdb=" N LEU A 540 " --> pdb=" O PRO A 536 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASN A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N VAL A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 619 through 646 removed outlier: 3.612A pdb=" N PHE A 624 " --> pdb=" O TRP A 620 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 626 " --> pdb=" O GLN A 622 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.561A pdb=" N ILE A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.518A pdb=" N PHE A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.624A pdb=" N LEU A 716 " --> pdb=" O SER A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.926A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 758 through 777 removed outlier: 4.044A pdb=" N PHE A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 797 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 832 Processing helix chain 'A' and resid 843 through 874 Proline residue: A 853 - end of helix removed outlier: 4.644A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 411 through 430 Processing helix chain 'B' and resid 435 through 455 Processing helix chain 'B' and resid 458 through 474 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 Processing helix chain 'B' and resid 499 through 518 removed outlier: 3.515A pdb=" N MET B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 4.133A pdb=" N LEU B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.983A pdb=" N MET B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 4.153A pdb=" N ALA B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 603 through 614 removed outlier: 3.939A pdb=" N SER B 611 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR B 612 " --> pdb=" O ILE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 626 through 647 removed outlier: 3.876A pdb=" N SER B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 683 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 698 Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.946A pdb=" N ILE B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 719 removed outlier: 3.590A pdb=" N LEU B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 741 removed outlier: 4.051A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 754 Processing helix chain 'B' and resid 758 through 777 removed outlier: 3.646A pdb=" N LEU B 769 " --> pdb=" O ILE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 797 removed outlier: 3.751A pdb=" N ILE B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.293A pdb=" N SER B 815 " --> pdb=" O ALA B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 832 Processing helix chain 'B' and resid 843 through 864 removed outlier: 4.567A pdb=" N VAL B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Proline residue: B 853 - end of helix Processing helix chain 'B' and resid 864 through 874 503 hydrogen bonds defined for protein. 1500 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: 1.96 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2117 1.34 - 1.46: 1625 1.46 - 1.58: 3473 1.58 - 1.69: 1 1.69 - 1.81: 86 Bond restraints: 7302 Sorted by residual: bond pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.14e+00 bond pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.57e+00 bond pdb=" N ILE A 420 " pdb=" CA ILE A 420 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N THR A 424 " pdb=" CA THR A 424 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.12e+00 ... (remaining 7297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 9770 1.81 - 3.62: 117 3.62 - 5.42: 34 5.42 - 7.23: 4 7.23 - 9.04: 1 Bond angle restraints: 9926 Sorted by residual: angle pdb=" CA PRO B 800 " pdb=" N PRO B 800 " pdb=" CD PRO B 800 " ideal model delta sigma weight residual 112.00 105.52 6.48 1.40e+00 5.10e-01 2.14e+01 angle pdb=" CA MET B 635 " pdb=" CB MET B 635 " pdb=" CG MET B 635 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N LEU A 426 " pdb=" CA LEU A 426 " pdb=" C LEU A 426 " ideal model delta sigma weight residual 111.07 107.67 3.40 1.07e+00 8.73e-01 1.01e+01 angle pdb=" C ILE B 863 " pdb=" N THR B 864 " pdb=" CA THR B 864 " ideal model delta sigma weight residual 122.56 117.83 4.73 1.50e+00 4.44e-01 9.94e+00 angle pdb=" N ILE B 601 " pdb=" CA ILE B 601 " pdb=" C ILE B 601 " ideal model delta sigma weight residual 111.91 109.13 2.78 8.90e-01 1.26e+00 9.79e+00 ... (remaining 9921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3673 17.48 - 34.95: 499 34.95 - 52.43: 113 52.43 - 69.90: 15 69.90 - 87.38: 6 Dihedral angle restraints: 4306 sinusoidal: 1574 harmonic: 2732 Sorted by residual: dihedral pdb=" CA MET B 597 " pdb=" C MET B 597 " pdb=" N SER B 598 " pdb=" CA SER B 598 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " pdb=" CD GLU A 513 " pdb=" OE1 GLU A 513 " ideal model delta sinusoidal sigma weight residual 0.00 87.38 -87.38 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N LYS B 752 " pdb=" CA LYS B 752 " pdb=" CB LYS B 752 " pdb=" CG LYS B 752 " ideal model delta sinusoidal sigma weight residual -60.00 -116.13 56.13 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 896 0.038 - 0.075: 248 0.075 - 0.113: 78 0.113 - 0.150: 5 0.150 - 0.188: 6 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ILE A 420 " pdb=" N ILE A 420 " pdb=" C ILE A 420 " pdb=" CB ILE A 420 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA LEU A 426 " pdb=" N LEU A 426 " pdb=" C LEU A 426 " pdb=" CB LEU A 426 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1230 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 799 " -0.060 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO B 800 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 800 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 800 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 862 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C VAL B 862 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL B 862 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE B 863 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 603 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 604 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 604 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 604 " -0.022 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 955 2.75 - 3.29: 7375 3.29 - 3.83: 12290 3.83 - 4.36: 14118 4.36 - 4.90: 24727 Nonbonded interactions: 59465 Sorted by model distance: nonbonded pdb=" OE1 GLU B 684 " pdb=" OG SER B 694 " model vdw 2.214 3.040 nonbonded pdb=" O ASN B 593 " pdb=" OG SER B 815 " model vdw 2.226 3.040 nonbonded pdb=" O GLY B 595 " pdb=" OG SER B 602 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 707 " pdb=" NZ LYS B 413 " model vdw 2.269 3.120 nonbonded pdb=" O MET A 552 " pdb=" OG SER A 599 " model vdw 2.277 3.040 ... (remaining 59460 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 407 through 877) } 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=0.00 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: 4.660 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.003 0.111 7302 Z= 0.197 Angle : 0.546 9.038 9926 Z= 0.305 Chirality : 0.039 0.188 1233 Planarity : 0.005 0.087 1185 Dihedral : 16.594 87.379 2546 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 27.35 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 947 helix: 1.66 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.92 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.001 0.001 HIS B 460 PHE 0.014 0.001 PHE A 643 TYR 0.006 0.001 TYR B 867 ARG 0.004 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.730 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 91 average time/residue: 0.1579 time to fit residues: 20.6533 Evaluate side-chains 91 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 552 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102064 restraints weight = 10927.852| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.74 r_work: 0.3268 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7302 Z= 0.207 Angle : 0.514 5.841 9926 Z= 0.265 Chirality : 0.038 0.127 1233 Planarity : 0.004 0.045 1185 Dihedral : 4.074 48.990 987 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 25.16 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.28), residues: 947 helix: 1.89 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 527 HIS 0.005 0.001 HIS B 439 PHE 0.016 0.001 PHE A 643 TYR 0.010 0.001 TYR B 518 ARG 0.003 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.795 Fit side-chains REVERT: B 446 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8791 (tm-30) REVERT: B 635 MET cc_start: 0.7727 (tmm) cc_final: 0.7388 (ttm) REVERT: B 795 ASP cc_start: 0.7673 (t0) cc_final: 0.7455 (t0) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 0.1496 time to fit residues: 23.5094 Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101894 restraints weight = 11062.933| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.78 r_work: 0.3256 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7302 Z= 0.182 Angle : 0.507 6.422 9926 Z= 0.259 Chirality : 0.038 0.187 1233 Planarity : 0.004 0.039 1185 Dihedral : 3.794 36.630 985 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.10 % Allowed : 25.68 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.28), residues: 947 helix: 2.00 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.99 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 527 HIS 0.004 0.001 HIS B 439 PHE 0.016 0.001 PHE A 643 TYR 0.009 0.001 TYR B 518 ARG 0.010 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 801 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7938 (mtpt) REVERT: B 635 MET cc_start: 0.7736 (tmm) cc_final: 0.7516 (ttm) REVERT: B 643 PHE cc_start: 0.7542 (t80) cc_final: 0.7291 (t80) REVERT: B 795 ASP cc_start: 0.7735 (t0) cc_final: 0.7425 (t0) REVERT: B 796 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7649 (mmtm) outliers start: 24 outliers final: 11 residues processed: 104 average time/residue: 0.1798 time to fit residues: 26.5621 Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 796 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.0020 chunk 75 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104691 restraints weight = 11064.802| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.74 r_work: 0.3299 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7302 Z= 0.142 Angle : 0.489 5.550 9926 Z= 0.249 Chirality : 0.038 0.192 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.752 39.360 985 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.71 % Allowed : 25.55 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.28), residues: 947 helix: 2.11 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 527 HIS 0.003 0.001 HIS A 439 PHE 0.012 0.001 PHE A 643 TYR 0.007 0.001 TYR B 518 ARG 0.007 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.711 Fit side-chains REVERT: A 801 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7960 (mtpt) REVERT: B 795 ASP cc_start: 0.7764 (t0) cc_final: 0.7440 (t0) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 0.1664 time to fit residues: 24.2013 Evaluate side-chains 98 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101215 restraints weight = 11092.325| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.78 r_work: 0.3243 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7302 Z= 0.258 Angle : 0.531 6.321 9926 Z= 0.271 Chirality : 0.039 0.192 1233 Planarity : 0.004 0.041 1185 Dihedral : 3.933 42.541 985 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.26 % Allowed : 24.52 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.28), residues: 947 helix: 1.99 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 620 HIS 0.004 0.002 HIS B 460 PHE 0.020 0.001 PHE A 643 TYR 0.013 0.001 TYR A 518 ARG 0.006 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: B 464 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: B 524 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 795 ASP cc_start: 0.7825 (t0) cc_final: 0.7547 (t0) outliers start: 33 outliers final: 20 residues processed: 112 average time/residue: 0.1668 time to fit residues: 26.6220 Evaluate side-chains 107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102374 restraints weight = 11075.184| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.74 r_work: 0.3260 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7302 Z= 0.208 Angle : 0.529 10.231 9926 Z= 0.266 Chirality : 0.039 0.198 1233 Planarity : 0.004 0.039 1185 Dihedral : 3.980 46.828 985 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.26 % Allowed : 23.87 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.28), residues: 947 helix: 2.02 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 620 HIS 0.005 0.001 HIS A 439 PHE 0.016 0.001 PHE A 643 TYR 0.010 0.001 TYR A 518 ARG 0.009 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 524 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 795 ASP cc_start: 0.7820 (t0) cc_final: 0.7523 (t0) outliers start: 33 outliers final: 23 residues processed: 110 average time/residue: 0.1606 time to fit residues: 25.8150 Evaluate side-chains 109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 67 optimal weight: 0.0470 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104448 restraints weight = 11088.733| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.74 r_work: 0.3295 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7302 Z= 0.142 Angle : 0.507 9.278 9926 Z= 0.256 Chirality : 0.038 0.213 1233 Planarity : 0.004 0.037 1185 Dihedral : 3.942 50.298 985 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.74 % Allowed : 24.77 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.28), residues: 947 helix: 2.17 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.009 0.002 HIS A 439 PHE 0.012 0.001 PHE A 643 TYR 0.006 0.001 TYR A 518 ARG 0.006 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.713 Fit side-chains REVERT: B 464 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: B 524 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8035 (mp) REVERT: B 635 MET cc_start: 0.7632 (tmm) cc_final: 0.7069 (ttm) REVERT: B 795 ASP cc_start: 0.7789 (t0) cc_final: 0.7459 (t0) outliers start: 29 outliers final: 19 residues processed: 104 average time/residue: 0.1502 time to fit residues: 22.7710 Evaluate side-chains 105 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104565 restraints weight = 11125.265| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.75 r_work: 0.3298 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7302 Z= 0.152 Angle : 0.511 10.669 9926 Z= 0.256 Chirality : 0.038 0.216 1233 Planarity : 0.004 0.037 1185 Dihedral : 3.901 49.926 985 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.35 % Allowed : 25.29 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 947 helix: 2.22 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.90 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 553 HIS 0.009 0.002 HIS A 439 PHE 0.012 0.001 PHE A 643 TYR 0.008 0.001 TYR B 518 ARG 0.007 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.818 Fit side-chains REVERT: B 464 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: B 524 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 635 MET cc_start: 0.7631 (tmm) cc_final: 0.7249 (ttm) REVERT: B 795 ASP cc_start: 0.7767 (t0) cc_final: 0.7438 (t0) outliers start: 26 outliers final: 21 residues processed: 105 average time/residue: 0.1504 time to fit residues: 23.2871 Evaluate side-chains 108 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102613 restraints weight = 11181.325| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.72 r_work: 0.3267 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7302 Z= 0.214 Angle : 0.534 8.496 9926 Z= 0.269 Chirality : 0.039 0.200 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.993 51.700 985 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.48 % Allowed : 24.65 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.28), residues: 947 helix: 2.14 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 553 HIS 0.009 0.002 HIS A 439 PHE 0.017 0.001 PHE A 643 TYR 0.011 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.740 Fit side-chains REVERT: B 464 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: B 524 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (mp) REVERT: B 635 MET cc_start: 0.7700 (tmm) cc_final: 0.7360 (ttm) REVERT: B 795 ASP cc_start: 0.7771 (t0) cc_final: 0.7454 (t0) outliers start: 27 outliers final: 22 residues processed: 107 average time/residue: 0.1506 time to fit residues: 24.4343 Evaluate side-chains 111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103208 restraints weight = 11277.109| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.77 r_work: 0.3279 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7302 Z= 0.182 Angle : 0.526 8.583 9926 Z= 0.265 Chirality : 0.039 0.206 1233 Planarity : 0.004 0.037 1185 Dihedral : 4.022 53.952 985 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.35 % Allowed : 25.29 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.28), residues: 947 helix: 2.16 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 PHE 0.014 0.001 PHE A 643 TYR 0.008 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.796 Fit side-chains REVERT: B 464 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: B 524 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 635 MET cc_start: 0.7664 (tmm) cc_final: 0.7347 (ttm) REVERT: B 795 ASP cc_start: 0.7787 (t0) cc_final: 0.7460 (t0) outliers start: 26 outliers final: 22 residues processed: 101 average time/residue: 0.1446 time to fit residues: 21.8905 Evaluate side-chains 107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104044 restraints weight = 11004.497| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.74 r_work: 0.3291 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7302 Z= 0.162 Angle : 0.532 12.716 9926 Z= 0.264 Chirality : 0.039 0.207 1233 Planarity : 0.004 0.037 1185 Dihedral : 4.027 55.770 985 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.35 % Allowed : 25.42 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 947 helix: 2.21 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 PHE 0.013 0.001 PHE A 643 TYR 0.009 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3719.40 seconds wall clock time: 69 minutes 12.72 seconds (4152.72 seconds total)