Starting phenix.real_space_refine on Wed Feb 12 03:16:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3q_35154/02_2025/8i3q_35154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3q_35154/02_2025/8i3q_35154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3q_35154/02_2025/8i3q_35154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3q_35154/02_2025/8i3q_35154.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3q_35154/02_2025/8i3q_35154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3q_35154/02_2025/8i3q_35154.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 95 5.49 5 S 12 5.16 5 C 4057 2.51 5 N 1312 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6998 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2026 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 44, 'rna3p_pyr': 39} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain breaks: 1 Chain: "A" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4971 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 556} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6549 SG CYS A 711 29.245 14.332 41.891 1.00 82.48 S ATOM 6569 SG CYS A 714 27.687 10.896 43.793 1.00 85.07 S ATOM 6757 SG CYS A 735 31.613 10.871 41.848 1.00 98.72 S ATOM 6776 SG CYS A 738 28.630 10.360 40.525 1.00 97.60 S Time building chain proxies: 4.68, per 1000 atoms: 0.67 Number of scatterers: 6998 At special positions: 0 Unit cell: (85.68, 91.56, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 12 16.00 P 95 15.00 O 1521 8.00 N 1312 7.00 C 4057 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: 2.35 Conformation dependent library (CDL) restraints added in 678.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 738 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 711 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 735 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 714 " Number of angles added : 6 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 50.6% alpha, 8.2% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 35 through 65 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.636A pdb=" N SER A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 142 through 154 removed outlier: 4.258A pdb=" N ASP A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 200 removed outlier: 4.619A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ALA A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 200 " --> pdb=" O TRP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.153A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.526A pdb=" N GLU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.803A pdb=" N LEU A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.523A pdb=" N LYS A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 595 removed outlier: 3.515A pdb=" N HIS A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 647 removed outlier: 3.851A pdb=" N ASN A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.533A pdb=" N ASP A 669 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.604A pdb=" N ARG A 674 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.521A pdb=" N ILE A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 722 through 729 removed outlier: 3.998A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.723A pdb=" N TRP A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 389 removed outlier: 6.819A pdb=" N ARG A 453 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 439 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A 451 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 441 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG A 449 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE A 443 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 402 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511 removed outlier: 6.867A pdb=" N LEU A 510 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 700 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 654 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 524 removed outlier: 4.032A pdb=" N GLN A 531 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.505A pdb=" N VAL A 538 " --> pdb=" O TYR A 544 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1385 1.33 - 1.45: 2200 1.45 - 1.57: 3566 1.57 - 1.69: 188 1.69 - 1.81: 17 Bond restraints: 7356 Sorted by residual: bond pdb=" N LYS A 73 " pdb=" CA LYS A 73 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.51e+01 bond pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 1.525 1.485 0.040 1.32e-02 5.74e+03 9.11e+00 bond pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.06e-02 8.90e+03 9.11e+00 bond pdb=" N VAL A 710 " pdb=" CA VAL A 710 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.22e-02 6.72e+03 8.06e+00 bond pdb=" N ARG A 382 " pdb=" CA ARG A 382 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 8.01e+00 ... (remaining 7351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 10117 2.45 - 4.91: 236 4.91 - 7.36: 20 7.36 - 9.81: 1 9.81 - 12.27: 2 Bond angle restraints: 10376 Sorted by residual: angle pdb=" N ALA A 482 " pdb=" CA ALA A 482 " pdb=" C ALA A 482 " ideal model delta sigma weight residual 113.23 104.26 8.97 1.24e+00 6.50e-01 5.23e+01 angle pdb=" N LEU A 358 " pdb=" CA LEU A 358 " pdb=" C LEU A 358 " ideal model delta sigma weight residual 111.36 104.29 7.07 1.09e+00 8.42e-01 4.20e+01 angle pdb=" CA GLN A 483 " pdb=" CB GLN A 483 " pdb=" CG GLN A 483 " ideal model delta sigma weight residual 114.10 123.92 -9.82 2.00e+00 2.50e-01 2.41e+01 angle pdb=" C PHE A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.84 114.25 5.59 1.25e+00 6.40e-01 2.00e+01 angle pdb=" C ARG A 47 " pdb=" N LYS A 48 " pdb=" CA LYS A 48 " ideal model delta sigma weight residual 120.44 126.05 -5.61 1.30e+00 5.92e-01 1.86e+01 ... (remaining 10371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 4206 34.82 - 69.63: 349 69.63 - 104.45: 45 104.45 - 139.27: 5 139.27 - 174.08: 5 Dihedral angle restraints: 4610 sinusoidal: 2866 harmonic: 1744 Sorted by residual: dihedral pdb=" CD ARG A 382 " pdb=" NE ARG A 382 " pdb=" CZ ARG A 382 " pdb=" NH1 ARG A 382 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" O4' C C 38 " pdb=" C1' C C 38 " pdb=" N1 C C 38 " pdb=" C2 C C 38 " ideal model delta sinusoidal sigma weight residual -160.00 9.75 -169.75 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U C 55 " pdb=" C1' U C 55 " pdb=" N1 U C 55 " pdb=" C2 U C 55 " ideal model delta sinusoidal sigma weight residual 200.00 48.63 151.37 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 4607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1030 0.068 - 0.135: 103 0.135 - 0.203: 27 0.203 - 0.270: 4 0.270 - 0.338: 3 Chirality restraints: 1167 Sorted by residual: chirality pdb=" CA PHE A 398 " pdb=" N PHE A 398 " pdb=" C PHE A 398 " pdb=" CB PHE A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ASN A 42 " pdb=" N ASN A 42 " pdb=" C ASN A 42 " pdb=" CB ASN A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA CYS A 714 " pdb=" N CYS A 714 " pdb=" C CYS A 714 " pdb=" CB CYS A 714 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1164 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 382 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG A 382 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 382 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 382 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 382 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 462 " -0.328 9.50e-02 1.11e+02 1.47e-01 1.32e+01 pdb=" NE ARG A 462 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 462 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 462 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 462 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 714 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C CYS A 714 " 0.049 2.00e-02 2.50e+03 pdb=" O CYS A 714 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 715 " -0.017 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 17 2.39 - 3.02: 3754 3.02 - 3.64: 11191 3.64 - 4.27: 16937 4.27 - 4.90: 25742 Nonbonded interactions: 57641 Sorted by model distance: nonbonded pdb=" NE2 GLN A 723 " pdb=" NZ LYS A 734 " model vdw 1.762 3.200 nonbonded pdb=" O2' G C 74 " pdb=" O5' A C 75 " model vdw 2.169 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" OH TYR A 155 " model vdw 2.263 3.120 nonbonded pdb=" NH1 ARG A 754 " pdb=" OE1 GLU A 759 " model vdw 2.276 3.120 nonbonded pdb=" O2' A C 76 " pdb=" OP1 G C 77 " model vdw 2.279 3.040 ... (remaining 57636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.270 Find NCS groups from input model: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.005 0.049 7356 Z= 0.312 Angle : 0.829 12.269 10376 Z= 0.510 Chirality : 0.049 0.338 1167 Planarity : 0.017 0.493 1002 Dihedral : 22.354 174.081 3470 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.39 % Allowed : 4.43 % Favored : 90.17 % 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: 0.08 (0.34), residues: 585 helix: 1.56 (0.31), residues: 267 sheet: -0.12 (0.62), residues: 70 loop : -1.64 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 632 HIS 0.004 0.001 HIS A 681 PHE 0.016 0.002 PHE A 398 TYR 0.013 0.002 TYR A 18 ARG 0.004 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.630 Fit side-chains REVERT: A 570 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6653 (mtp-110) outliers start: 28 outliers final: 10 residues processed: 105 average time/residue: 0.4271 time to fit residues: 51.6973 Evaluate side-chains 44 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A 485 GLN A 578 GLN A 636 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.143117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111298 restraints weight = 11838.700| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.90 r_work: 0.3501 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7356 Z= 0.166 Angle : 0.610 7.495 10376 Z= 0.312 Chirality : 0.037 0.225 1167 Planarity : 0.005 0.064 1002 Dihedral : 22.470 178.441 2169 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.89 % Allowed : 8.67 % Favored : 88.44 % 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: 0.80 (0.35), residues: 585 helix: 2.33 (0.31), residues: 263 sheet: -0.14 (0.62), residues: 67 loop : -1.29 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 632 HIS 0.002 0.001 HIS A 159 PHE 0.016 0.001 PHE A 81 TYR 0.014 0.001 TYR A 665 ARG 0.005 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.694 Fit side-chains REVERT: A 382 ARG cc_start: 0.7691 (mmm160) cc_final: 0.7341 (mmm-85) REVERT: A 568 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8637 (tt) outliers start: 15 outliers final: 3 residues processed: 49 average time/residue: 0.3168 time to fit residues: 19.4606 Evaluate side-chains 28 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.139002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105937 restraints weight = 12114.124| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.94 r_work: 0.3394 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7356 Z= 0.216 Angle : 0.631 7.458 10376 Z= 0.325 Chirality : 0.039 0.221 1167 Planarity : 0.005 0.068 1002 Dihedral : 22.167 176.815 2148 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.12 % Allowed : 12.72 % Favored : 85.16 % 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: 0.93 (0.35), residues: 585 helix: 2.40 (0.30), residues: 258 sheet: -0.42 (0.61), residues: 71 loop : -0.99 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.017 0.002 PHE A 50 TYR 0.010 0.002 TYR A 665 ARG 0.005 0.001 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.626 Fit side-chains REVERT: A 382 ARG cc_start: 0.7573 (mmm160) cc_final: 0.7248 (mmm-85) REVERT: A 568 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8676 (tt) outliers start: 11 outliers final: 5 residues processed: 42 average time/residue: 0.3522 time to fit residues: 18.0376 Evaluate side-chains 32 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 383 HIS A 485 GLN A 572 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.134441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102131 restraints weight = 11911.304| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.95 r_work: 0.3326 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7356 Z= 0.311 Angle : 0.706 7.446 10376 Z= 0.363 Chirality : 0.042 0.228 1167 Planarity : 0.006 0.057 1002 Dihedral : 22.293 179.549 2148 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.12 % Allowed : 15.22 % Favored : 82.66 % 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: 0.53 (0.35), residues: 585 helix: 2.00 (0.29), residues: 259 sheet: -0.72 (0.61), residues: 70 loop : -1.08 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 632 HIS 0.006 0.002 HIS A 159 PHE 0.020 0.003 PHE A 499 TYR 0.011 0.002 TYR A 359 ARG 0.004 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.673 Fit side-chains REVERT: A 382 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7269 (mmm-85) REVERT: A 568 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (tt) outliers start: 11 outliers final: 4 residues processed: 39 average time/residue: 0.3162 time to fit residues: 15.5159 Evaluate side-chains 31 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 576 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.140597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108882 restraints weight = 11983.693| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.92 r_work: 0.3441 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7356 Z= 0.136 Angle : 0.568 7.482 10376 Z= 0.290 Chirality : 0.036 0.220 1167 Planarity : 0.004 0.049 1002 Dihedral : 22.128 178.156 2148 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.35 % Allowed : 16.18 % Favored : 82.47 % 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: 1.18 (0.36), residues: 585 helix: 2.66 (0.30), residues: 259 sheet: -0.33 (0.60), residues: 74 loop : -0.92 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 632 HIS 0.002 0.000 HIS A 159 PHE 0.010 0.001 PHE A 756 TYR 0.012 0.001 TYR A 359 ARG 0.003 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.684 Fit side-chains REVERT: A 382 ARG cc_start: 0.7431 (mmm160) cc_final: 0.7129 (mmm-85) REVERT: A 568 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8550 (tt) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.3674 time to fit residues: 16.3456 Evaluate side-chains 29 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.138490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106432 restraints weight = 12083.170| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.93 r_work: 0.3411 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7356 Z= 0.155 Angle : 0.567 7.486 10376 Z= 0.289 Chirality : 0.036 0.220 1167 Planarity : 0.004 0.049 1002 Dihedral : 22.073 177.828 2148 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.54 % Allowed : 16.18 % Favored : 82.27 % 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: 1.32 (0.36), residues: 585 helix: 2.79 (0.30), residues: 259 sheet: -0.17 (0.61), residues: 76 loop : -0.90 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 632 HIS 0.002 0.001 HIS A 572 PHE 0.013 0.001 PHE A 50 TYR 0.011 0.001 TYR A 359 ARG 0.002 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.665 Fit side-chains REVERT: A 382 ARG cc_start: 0.7430 (mmm160) cc_final: 0.7103 (mmm-85) REVERT: A 568 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8543 (tt) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.3441 time to fit residues: 14.3360 Evaluate side-chains 30 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 46 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.143799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.112678 restraints weight = 12156.581| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.93 r_work: 0.3516 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7356 Z= 0.125 Angle : 0.529 7.484 10376 Z= 0.267 Chirality : 0.034 0.221 1167 Planarity : 0.004 0.046 1002 Dihedral : 21.979 178.997 2148 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.35 % Allowed : 16.57 % Favored : 82.08 % 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: 1.64 (0.37), residues: 585 helix: 3.01 (0.30), residues: 260 sheet: 0.11 (0.66), residues: 73 loop : -0.73 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 632 HIS 0.001 0.000 HIS A 458 PHE 0.008 0.001 PHE A 756 TYR 0.011 0.001 TYR A 359 ARG 0.003 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.663 Fit side-chains REVERT: A 382 ARG cc_start: 0.7374 (mmm160) cc_final: 0.7011 (mmm-85) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.3034 time to fit residues: 15.1150 Evaluate side-chains 30 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.140653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108838 restraints weight = 12222.428| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.95 r_work: 0.3444 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7356 Z= 0.137 Angle : 0.545 8.002 10376 Z= 0.272 Chirality : 0.035 0.220 1167 Planarity : 0.005 0.084 1002 Dihedral : 21.936 179.157 2148 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.96 % Allowed : 17.34 % Favored : 81.70 % 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: 1.67 (0.37), residues: 585 helix: 2.97 (0.30), residues: 261 sheet: 0.08 (0.65), residues: 73 loop : -0.63 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 632 HIS 0.002 0.001 HIS A 159 PHE 0.011 0.001 PHE A 50 TYR 0.010 0.001 TYR A 359 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.607 Fit side-chains REVERT: A 382 ARG cc_start: 0.7284 (mmm160) cc_final: 0.6922 (mmm-85) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.3001 time to fit residues: 12.7961 Evaluate side-chains 29 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 0.0370 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.141790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109909 restraints weight = 12308.391| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.97 r_work: 0.3450 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7356 Z= 0.134 Angle : 0.538 7.500 10376 Z= 0.269 Chirality : 0.034 0.220 1167 Planarity : 0.004 0.081 1002 Dihedral : 21.911 179.131 2148 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.96 % Allowed : 17.15 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.81 (0.37), residues: 585 helix: 3.10 (0.30), residues: 260 sheet: 0.18 (0.66), residues: 73 loop : -0.58 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 632 HIS 0.001 0.000 HIS A 572 PHE 0.010 0.001 PHE A 50 TYR 0.010 0.001 TYR A 359 ARG 0.002 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.567 Fit side-chains REVERT: A 382 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6897 (mmm-85) REVERT: A 665 TYR cc_start: 0.8146 (t80) cc_final: 0.7919 (t80) outliers start: 5 outliers final: 5 residues processed: 30 average time/residue: 0.3241 time to fit residues: 12.3817 Evaluate side-chains 29 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 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 = 0.4088 r_free = 0.4088 target = 0.140954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108954 restraints weight = 12383.750| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.97 r_work: 0.3433 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7356 Z= 0.140 Angle : 0.542 7.505 10376 Z= 0.271 Chirality : 0.034 0.220 1167 Planarity : 0.004 0.078 1002 Dihedral : 21.898 179.824 2148 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.96 % Allowed : 16.96 % Favored : 82.08 % 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: 1.79 (0.37), residues: 585 helix: 3.12 (0.30), residues: 258 sheet: 0.13 (0.66), residues: 73 loop : -0.58 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 632 HIS 0.002 0.000 HIS A 572 PHE 0.011 0.001 PHE A 50 TYR 0.009 0.001 TYR A 359 ARG 0.002 0.000 ARG A 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.599 Fit side-chains REVERT: A 382 ARG cc_start: 0.7202 (mmm160) cc_final: 0.6817 (mmm-85) REVERT: A 665 TYR cc_start: 0.8117 (t80) cc_final: 0.7893 (t80) REVERT: A 761 GLU cc_start: 0.7334 (pt0) cc_final: 0.6797 (mm-30) outliers start: 5 outliers final: 5 residues processed: 35 average time/residue: 0.3397 time to fit residues: 14.8854 Evaluate side-chains 32 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.139393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.106981 restraints weight = 12303.367| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.98 r_work: 0.3400 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7356 Z= 0.158 Angle : 0.553 7.490 10376 Z= 0.279 Chirality : 0.035 0.220 1167 Planarity : 0.005 0.076 1002 Dihedral : 21.919 178.693 2148 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.96 % Allowed : 17.15 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.37), residues: 585 helix: 3.00 (0.30), residues: 258 sheet: 0.06 (0.63), residues: 77 loop : -0.54 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 632 HIS 0.003 0.001 HIS A 572 PHE 0.013 0.001 PHE A 50 TYR 0.010 0.001 TYR A 359 ARG 0.002 0.000 ARG A 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.91 seconds wall clock time: 58 minutes 32.25 seconds (3512.25 seconds total)