Starting phenix.real_space_refine on Fri Aug 22 19:14:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r35_18861/08_2025/8r35_18861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r35_18861/08_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_18861/08_2025/8r35_18861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r35_18861/08_2025/8r35_18861.map" model { file = "/net/cci-nas-00/data/ceres_data/8r35_18861/08_2025/8r35_18861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r35_18861/08_2025/8r35_18861.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.71, per 1000 atoms: 0.24 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: 0.56 Conformation dependent library (CDL) restraints added in 365.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.14 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: 1.00 Time building geometry restraints manager: 0.78 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: 8.260 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.620 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.750 ------------------------------------------------------------------------------- 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= 0.148 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 840 TYR 0.006 0.001 TYR B 867 PHE 0.014 0.001 PHE A 643 TRP 0.008 0.001 TRP B 553 HIS 0.001 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7302) covalent geometry : angle 0.54550 ( 9926) hydrogen bonds : bond 0.16124 ( 503) hydrogen bonds : angle 6.43936 ( 1500) *********************** 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 : 0.304 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 91 average time/residue: 0.0695 time to fit residues: 9.2538 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 : 0.215 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 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 791 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101748 restraints weight = 11059.471| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.74 r_work: 0.3260 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0883 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= 0.145 Angle : 0.519 6.066 9926 Z= 0.268 Chirality : 0.039 0.128 1233 Planarity : 0.004 0.044 1185 Dihedral : 4.119 48.514 987 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.97 % Allowed : 24.90 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.28), residues: 947 helix: 1.85 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 840 TYR 0.011 0.001 TYR B 518 PHE 0.017 0.001 PHE A 643 TRP 0.010 0.001 TRP B 527 HIS 0.005 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7302) covalent geometry : angle 0.51890 ( 9926) hydrogen bonds : bond 0.04113 ( 503) hydrogen bonds : angle 4.38984 ( 1500) *********************** 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 118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.296 Fit side-chains REVERT: A 801 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7951 (mtpt) REVERT: B 446 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8794 (tm-30) REVERT: B 635 MET cc_start: 0.7787 (tmm) cc_final: 0.7432 (ttm) REVERT: B 795 ASP cc_start: 0.7689 (t0) cc_final: 0.7460 (t0) outliers start: 23 outliers final: 12 residues processed: 109 average time/residue: 0.0653 time to fit residues: 10.5356 Evaluate side-chains 100 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 801 LYS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 435 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 641 LEU 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 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.126933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102851 restraints weight = 10959.604| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.74 r_work: 0.3269 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1091 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= 0.114 Angle : 0.498 6.600 9926 Z= 0.255 Chirality : 0.038 0.186 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.782 37.176 985 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.97 % Allowed : 25.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.28), residues: 947 helix: 2.03 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 840 TYR 0.008 0.001 TYR B 518 PHE 0.014 0.001 PHE A 643 TRP 0.008 0.001 TRP B 527 HIS 0.004 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7302) covalent geometry : angle 0.49848 ( 9926) hydrogen bonds : bond 0.03678 ( 503) hydrogen bonds : angle 4.10406 ( 1500) *********************** 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 114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 635 MET cc_start: 0.7778 (tmm) cc_final: 0.7535 (ttm) REVERT: B 643 PHE cc_start: 0.7509 (t80) cc_final: 0.7270 (t80) REVERT: B 795 ASP cc_start: 0.7710 (t0) cc_final: 0.7379 (t0) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.0729 time to fit residues: 11.1053 Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104244 restraints weight = 11088.062| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.74 r_work: 0.3295 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7302 Z= 0.111 Angle : 0.488 5.346 9926 Z= 0.249 Chirality : 0.038 0.190 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.765 40.702 985 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.48 % Allowed : 24.52 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.28), residues: 947 helix: 2.11 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 840 TYR 0.008 0.001 TYR B 518 PHE 0.013 0.001 PHE A 643 TRP 0.008 0.001 TRP B 527 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7302) covalent geometry : angle 0.48784 ( 9926) hydrogen bonds : bond 0.03478 ( 503) hydrogen bonds : angle 3.96763 ( 1500) *********************** 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 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.289 Fit side-chains REVERT: B 524 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 795 ASP cc_start: 0.7736 (t0) cc_final: 0.7414 (t0) outliers start: 27 outliers final: 15 residues processed: 109 average time/residue: 0.0672 time to fit residues: 10.6643 Evaluate side-chains 102 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 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 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 3 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104119 restraints weight = 11038.236| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.75 r_work: 0.3291 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7302 Z= 0.113 Angle : 0.493 6.169 9926 Z= 0.250 Chirality : 0.038 0.199 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.807 42.167 985 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.87 % Allowed : 24.13 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.28), residues: 947 helix: 2.19 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.92 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 840 TYR 0.008 0.001 TYR B 518 PHE 0.014 0.001 PHE A 643 TRP 0.008 0.001 TRP B 553 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7302) covalent geometry : angle 0.49261 ( 9926) hydrogen bonds : bond 0.03454 ( 503) hydrogen bonds : angle 3.93123 ( 1500) *********************** 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 121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 524 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 795 ASP cc_start: 0.7752 (t0) cc_final: 0.7425 (t0) outliers start: 30 outliers final: 19 residues processed: 112 average time/residue: 0.0649 time to fit residues: 10.6665 Evaluate side-chains 107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 771 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 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 769 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 6.9990 chunk 81 optimal weight: 0.0770 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103420 restraints weight = 11114.896| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.75 r_work: 0.3275 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1351 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= 0.128 Angle : 0.509 6.751 9926 Z= 0.259 Chirality : 0.038 0.206 1233 Planarity : 0.004 0.039 1185 Dihedral : 3.838 44.296 985 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.00 % Allowed : 23.48 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.28), residues: 947 helix: 2.16 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 840 TYR 0.009 0.001 TYR A 518 PHE 0.015 0.001 PHE A 643 TRP 0.010 0.001 TRP B 553 HIS 0.009 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7302) covalent geometry : angle 0.50922 ( 9926) hydrogen bonds : bond 0.03583 ( 503) hydrogen bonds : angle 3.96296 ( 1500) *********************** 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 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.280 Fit side-chains REVERT: B 464 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: B 524 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 795 ASP cc_start: 0.7785 (t0) cc_final: 0.7459 (t0) outliers start: 31 outliers final: 21 residues processed: 111 average time/residue: 0.0574 time to fit residues: 9.4207 Evaluate side-chains 109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 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 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 839 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.128170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104046 restraints weight = 11139.218| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.73 r_work: 0.3286 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7302 Z= 0.118 Angle : 0.527 10.636 9926 Z= 0.263 Chirality : 0.038 0.209 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.874 46.487 985 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.87 % Allowed : 24.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.28), residues: 947 helix: 2.17 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.90 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 840 TYR 0.008 0.001 TYR A 518 PHE 0.014 0.001 PHE A 643 TRP 0.009 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7302) covalent geometry : angle 0.52662 ( 9926) hydrogen bonds : bond 0.03516 ( 503) hydrogen bonds : angle 3.92803 ( 1500) *********************** 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 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.253 Fit side-chains REVERT: B 464 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: B 524 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 635 MET cc_start: 0.7657 (tmm) cc_final: 0.7095 (ttm) REVERT: B 795 ASP cc_start: 0.7763 (t0) cc_final: 0.7432 (t0) outliers start: 30 outliers final: 23 residues processed: 106 average time/residue: 0.0567 time to fit residues: 8.9345 Evaluate side-chains 111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 839 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.0670 chunk 62 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 66 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.130983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106876 restraints weight = 11039.719| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.75 r_work: 0.3321 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7302 Z= 0.100 Angle : 0.503 9.955 9926 Z= 0.251 Chirality : 0.038 0.218 1233 Planarity : 0.004 0.037 1185 Dihedral : 3.819 49.123 985 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.45 % Allowed : 25.42 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.28), residues: 947 helix: 2.33 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 840 TYR 0.005 0.001 TYR B 518 PHE 0.008 0.001 PHE A 643 TRP 0.010 0.001 TRP B 553 HIS 0.008 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 7302) covalent geometry : angle 0.50293 ( 9926) hydrogen bonds : bond 0.03075 ( 503) hydrogen bonds : angle 3.74825 ( 1500) *********************** 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 110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.263 Fit side-chains REVERT: B 492 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 524 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8006 (mp) REVERT: B 635 MET cc_start: 0.7609 (tmm) cc_final: 0.7285 (ttm) REVERT: B 795 ASP cc_start: 0.7723 (t0) cc_final: 0.7383 (t0) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.0565 time to fit residues: 8.8190 Evaluate side-chains 103 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 771 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 48 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 = 0.3705 r_free = 0.3705 target = 0.128644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104339 restraints weight = 11081.288| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.74 r_work: 0.3290 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7302 Z= 0.123 Angle : 0.527 9.659 9926 Z= 0.263 Chirality : 0.038 0.215 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.892 49.923 985 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.58 % Allowed : 25.16 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.28), residues: 947 helix: 2.30 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 840 TYR 0.010 0.001 TYR A 518 PHE 0.015 0.001 PHE A 643 TRP 0.016 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7302) covalent geometry : angle 0.52726 ( 9926) hydrogen bonds : bond 0.03513 ( 503) hydrogen bonds : angle 3.87527 ( 1500) *********************** 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 106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.236 Fit side-chains REVERT: B 464 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: B 524 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8030 (mp) REVERT: B 635 MET cc_start: 0.7641 (tmm) cc_final: 0.7369 (ttm) REVERT: B 795 ASP cc_start: 0.7727 (t0) cc_final: 0.7395 (t0) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.0573 time to fit residues: 8.6508 Evaluate side-chains 101 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 771 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 45 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.128983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104598 restraints weight = 11070.392| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.74 r_work: 0.3301 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7302 Z= 0.113 Angle : 0.539 11.452 9926 Z= 0.264 Chirality : 0.039 0.236 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.902 51.505 985 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 : 2.45 % Allowed : 25.94 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.28), residues: 947 helix: 2.30 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 840 TYR 0.008 0.001 TYR B 518 PHE 0.012 0.001 PHE A 643 TRP 0.018 0.001 TRP B 553 HIS 0.007 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7302) covalent geometry : angle 0.53864 ( 9926) hydrogen bonds : bond 0.03411 ( 503) hydrogen bonds : angle 3.85177 ( 1500) ********************** 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 101 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.274 Fit side-chains REVERT: B 464 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: B 492 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 635 MET cc_start: 0.7648 (tmm) cc_final: 0.7383 (ttm) REVERT: B 795 ASP cc_start: 0.7714 (t0) cc_final: 0.7383 (t0) outliers start: 19 outliers final: 15 residues processed: 93 average time/residue: 0.0507 time to fit residues: 7.2315 Evaluate side-chains 98 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 771 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.128932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104630 restraints weight = 11085.580| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.74 r_work: 0.3282 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1681 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= 0.113 Angle : 0.536 9.661 9926 Z= 0.263 Chirality : 0.039 0.246 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.944 55.078 985 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 26.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.28), residues: 947 helix: 2.32 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 840 TYR 0.008 0.001 TYR B 518 PHE 0.013 0.001 PHE A 643 TRP 0.022 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7302) covalent geometry : angle 0.53601 ( 9926) hydrogen bonds : bond 0.03403 ( 503) hydrogen bonds : angle 3.84900 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.28 seconds wall clock time: 32 minutes 34.61 seconds (1954.61 seconds total)