Starting phenix.real_space_refine on Tue Feb 11 19:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nxf_12638/02_2025/7nxf_12638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nxf_12638/02_2025/7nxf_12638.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/7nxf_12638/02_2025/7nxf_12638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nxf_12638/02_2025/7nxf_12638.map" model { file = "/net/cci-nas-00/data/ceres_data/7nxf_12638/02_2025/7nxf_12638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nxf_12638/02_2025/7nxf_12638.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= 0.001 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 2 5.49 5 Mg 1 5.21 5 S 23 5.16 5 C 4130 2.51 5 N 1060 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6405 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.69, per 1000 atoms: 0.73 Number of scatterers: 6405 At special positions: 0 Unit cell: (92.07, 72.819, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 23 16.00 P 2 15.00 Mg 1 11.99 O 1188 8.00 N 1060 7.00 C 4130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 946.5 milliseconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 52.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 83 " --> pdb=" O LEU A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 315 Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.619A pdb=" N VAL A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.518A pdb=" N GLN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 593 through 603 removed outlier: 3.822A pdb=" N ASP A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 625 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET A 777 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 807 Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 824 through 845 Processing helix chain 'A' and resid 853 through 878 removed outlier: 3.661A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 919 Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL A 204 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 256 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN A 224 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 250 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL A 629 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE A 649 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET A 631 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 374 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 632 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 376 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 375 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 557 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 377 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 579 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE A 526 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG A 517 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A 528 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 1011 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: 1.91 Time building geometry restraints manager: 1.83 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: 1504 1.33 - 1.45: 1404 1.45 - 1.58: 3585 1.58 - 1.70: 0 1.70 - 1.83: 40 Bond restraints: 6533 Sorted by residual: bond pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sigma weight residual 1.610 1.808 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C5 ADP A1001 " pdb=" C6 ADP A1001 " ideal model delta sigma weight residual 1.490 1.401 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C8 ADP A1001 " pdb=" N9 ADP A1001 " ideal model delta sigma weight residual 1.337 1.409 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " ideal model delta sigma weight residual 1.426 1.354 0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 6528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 8832 3.96 - 7.92: 33 7.92 - 11.88: 5 11.88 - 15.84: 5 15.84 - 19.80: 1 Bond angle restraints: 8876 Sorted by residual: angle pdb=" O1A ADP A1001 " pdb=" PA ADP A1001 " pdb=" O5' ADP A1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O2A ADP A1001 " pdb=" PA ADP A1001 " pdb=" O3A ADP A1001 " ideal model delta sigma weight residual 108.20 123.77 -15.57 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sigma weight residual 120.50 105.39 15.11 3.00e+00 1.11e-01 2.54e+01 angle pdb=" PA ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sigma weight residual 120.50 106.19 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" O3B ADP A1001 " ideal model delta sigma weight residual 108.20 94.68 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 8871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.30: 3744 30.30 - 60.60: 109 60.60 - 90.90: 4 90.90 - 121.20: 0 121.20 - 151.50: 2 Dihedral angle restraints: 3859 sinusoidal: 1498 harmonic: 2361 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 74.18 -134.18 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" CA VAL A 93 " pdb=" C VAL A 93 " pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta harmonic sigma weight residual 180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 3856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 685 0.038 - 0.076: 264 0.076 - 0.114: 73 0.114 - 0.152: 13 0.152 - 0.190: 4 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C2' ADP A1001 " pdb=" C1' ADP A1001 " pdb=" C3' ADP A1001 " pdb=" O2' ADP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CB THR A 267 " pdb=" CA THR A 267 " pdb=" OG1 THR A 267 " pdb=" CG2 THR A 267 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CG LEU A 702 " pdb=" CB LEU A 702 " pdb=" CD1 LEU A 702 " pdb=" CD2 LEU A 702 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 1036 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 709 " 0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP A 709 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 709 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 709 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 709 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 709 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 709 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 592 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 593 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 846 " -0.023 2.00e-02 2.50e+03 1.89e-02 8.94e+00 pdb=" CG TRP A 846 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 846 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 846 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 846 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 846 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 846 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 846 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 846 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 846 " -0.003 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 2206 2.85 - 3.42: 7232 3.42 - 4.00: 11393 4.00 - 4.57: 16530 4.57 - 5.14: 23451 Nonbonded interactions: 60812 Sorted by model distance: nonbonded pdb=" O PHE A 246 " pdb=" OG SER A 249 " model vdw 2.281 3.040 nonbonded pdb=" O THR A 773 " pdb=" OG1 THR A 776 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU A 602 " pdb=" OH TYR A 627 " model vdw 2.388 3.040 nonbonded pdb=" O4' ADP A1001 " pdb=" O5' ADP A1001 " model vdw 2.391 2.432 nonbonded pdb=" OD2 ASP A 403 " pdb=" OG1 THR A 407 " model vdw 2.394 3.040 ... (remaining 60807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 0.010 Normalize map: mean=0, sd=1: 3.030 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: 0.040 Set scattering table: 0.060 Process input model: 18.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.006 0.216 6533 Z= 0.401 Angle : 0.816 19.804 8876 Z= 0.391 Chirality : 0.044 0.190 1039 Planarity : 0.005 0.082 1118 Dihedral : 14.198 151.503 2345 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.71 (0.29), residues: 823 helix: 0.88 (0.25), residues: 424 sheet: -1.48 (0.68), residues: 53 loop : -2.07 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 709 HIS 0.006 0.001 HIS A 701 PHE 0.012 0.001 PHE A 841 TYR 0.016 0.002 TYR A 691 ARG 0.003 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7979 (mmmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2759 time to fit residues: 26.9723 Evaluate side-chains 44 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.094819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065559 restraints weight = 18626.959| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.31 r_work: 0.3098 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6533 Z= 0.187 Angle : 0.650 7.730 8876 Z= 0.326 Chirality : 0.042 0.143 1039 Planarity : 0.004 0.056 1118 Dihedral : 8.246 136.456 888 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.02 % Allowed : 8.63 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.29), residues: 823 helix: 1.40 (0.26), residues: 429 sheet: -1.44 (0.67), residues: 53 loop : -2.32 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 709 HIS 0.006 0.001 HIS A 701 PHE 0.008 0.001 PHE A 868 TYR 0.017 0.001 TYR A 691 ARG 0.006 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8028 (p90) cc_final: 0.7092 (p90) REVERT: A 444 LYS cc_start: 0.7614 (mmmt) cc_final: 0.7287 (mmmt) REVERT: A 469 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8130 (mmm160) REVERT: A 496 GLN cc_start: 0.8606 (pp30) cc_final: 0.8376 (pm20) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.2157 time to fit residues: 16.7042 Evaluate side-chains 53 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.093925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064135 restraints weight = 18798.180| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.31 r_work: 0.3078 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6533 Z= 0.185 Angle : 0.603 6.438 8876 Z= 0.303 Chirality : 0.041 0.135 1039 Planarity : 0.004 0.056 1118 Dihedral : 7.840 131.955 888 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.75 % Allowed : 10.53 % Favored : 87.72 % 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: -0.07 (0.30), residues: 823 helix: 1.79 (0.26), residues: 428 sheet: -1.72 (0.63), residues: 55 loop : -2.31 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.006 0.001 HIS A 701 PHE 0.008 0.001 PHE A 286 TYR 0.015 0.001 TYR A 691 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8071 (p90) cc_final: 0.7782 (p90) REVERT: A 444 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7429 (mmmt) REVERT: A 469 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8056 (mmm160) REVERT: A 496 GLN cc_start: 0.8709 (pp30) cc_final: 0.8416 (pm20) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.1792 time to fit residues: 14.1530 Evaluate side-chains 56 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 806 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.090359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060428 restraints weight = 19491.740| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.32 r_work: 0.2957 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6533 Z= 0.374 Angle : 0.659 5.834 8876 Z= 0.331 Chirality : 0.043 0.131 1039 Planarity : 0.004 0.051 1118 Dihedral : 7.695 125.969 888 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.63 % Allowed : 11.55 % Favored : 85.82 % 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: -0.03 (0.30), residues: 823 helix: 1.77 (0.26), residues: 442 sheet: -1.83 (0.61), residues: 54 loop : -2.35 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 846 HIS 0.006 0.001 HIS A 701 PHE 0.013 0.001 PHE A 705 TYR 0.014 0.002 TYR A 691 ARG 0.002 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8076 (p90) cc_final: 0.7721 (p90) REVERT: A 444 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7500 (mmmt) REVERT: A 469 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7957 (mmm160) outliers start: 18 outliers final: 10 residues processed: 53 average time/residue: 0.1992 time to fit residues: 15.4917 Evaluate side-chains 53 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.091818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061757 restraints weight = 18847.182| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.30 r_work: 0.2999 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6533 Z= 0.211 Angle : 0.583 6.111 8876 Z= 0.292 Chirality : 0.041 0.133 1039 Planarity : 0.004 0.050 1118 Dihedral : 7.409 124.119 888 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.19 % Allowed : 12.72 % Favored : 85.09 % 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: 0.18 (0.30), residues: 823 helix: 1.97 (0.26), residues: 439 sheet: -1.88 (0.60), residues: 57 loop : -2.24 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 846 HIS 0.006 0.001 HIS A 701 PHE 0.009 0.001 PHE A 841 TYR 0.015 0.001 TYR A 691 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8206 (p90) cc_final: 0.7838 (p90) REVERT: A 444 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7533 (mmmt) REVERT: A 469 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7994 (mmm160) REVERT: A 496 GLN cc_start: 0.9048 (pp30) cc_final: 0.8828 (pp30) REVERT: A 533 MET cc_start: 0.8184 (ttt) cc_final: 0.7964 (ppp) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.2026 time to fit residues: 14.3342 Evaluate side-chains 55 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 37 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.092076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.062433 restraints weight = 18879.528| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.25 r_work: 0.3009 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6533 Z= 0.203 Angle : 0.583 7.249 8876 Z= 0.290 Chirality : 0.041 0.133 1039 Planarity : 0.003 0.045 1118 Dihedral : 7.127 120.242 888 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.63 % Allowed : 14.04 % Favored : 83.33 % 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: 0.34 (0.30), residues: 823 helix: 2.15 (0.26), residues: 438 sheet: -1.95 (0.60), residues: 57 loop : -2.20 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 846 HIS 0.006 0.001 HIS A 701 PHE 0.008 0.001 PHE A 841 TYR 0.014 0.001 TYR A 691 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8234 (p90) cc_final: 0.7931 (p90) REVERT: A 444 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7574 (mmmt) REVERT: A 469 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7987 (mmm160) outliers start: 18 outliers final: 11 residues processed: 55 average time/residue: 0.2017 time to fit residues: 15.2278 Evaluate side-chains 55 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 TYR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.089308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058929 restraints weight = 19367.657| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.39 r_work: 0.2938 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6533 Z= 0.379 Angle : 0.646 7.300 8876 Z= 0.323 Chirality : 0.043 0.141 1039 Planarity : 0.004 0.046 1118 Dihedral : 7.148 117.977 888 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.34 % Allowed : 14.04 % Favored : 83.63 % 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: 0.17 (0.30), residues: 823 helix: 2.02 (0.26), residues: 438 sheet: -1.86 (0.62), residues: 56 loop : -2.31 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 846 HIS 0.006 0.001 HIS A 701 PHE 0.014 0.001 PHE A 705 TYR 0.013 0.001 TYR A 691 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8239 (p90) cc_final: 0.7812 (p90) REVERT: A 444 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7525 (mmmt) REVERT: A 469 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7927 (mmm160) REVERT: A 778 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8676 (m-10) outliers start: 16 outliers final: 12 residues processed: 50 average time/residue: 0.2128 time to fit residues: 14.4534 Evaluate side-chains 53 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 778 TYR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.091600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.061669 restraints weight = 18966.806| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.39 r_work: 0.3030 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6533 Z= 0.181 Angle : 0.586 8.624 8876 Z= 0.288 Chirality : 0.040 0.141 1039 Planarity : 0.003 0.043 1118 Dihedral : 6.898 119.445 888 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.19 % Allowed : 14.33 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 823 helix: 2.17 (0.26), residues: 439 sheet: -1.91 (0.60), residues: 58 loop : -2.14 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 846 HIS 0.005 0.001 HIS A 701 PHE 0.008 0.001 PHE A 841 TYR 0.014 0.001 TYR A 691 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8259 (p90) cc_final: 0.8015 (p90) REVERT: A 444 LYS cc_start: 0.7824 (mmmt) cc_final: 0.7613 (mtmm) REVERT: A 469 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7951 (mmm160) REVERT: A 800 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8644 (tm-30) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 0.2044 time to fit residues: 15.2706 Evaluate side-chains 54 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 TYR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 874 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.091815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.062319 restraints weight = 19248.075| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.40 r_work: 0.3051 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6533 Z= 0.165 Angle : 0.570 7.932 8876 Z= 0.278 Chirality : 0.041 0.198 1039 Planarity : 0.003 0.044 1118 Dihedral : 6.649 123.024 888 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.75 % Allowed : 15.06 % Favored : 83.19 % 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: 0.46 (0.31), residues: 823 helix: 2.24 (0.26), residues: 439 sheet: -1.86 (0.60), residues: 58 loop : -2.14 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 846 HIS 0.011 0.001 HIS A 701 PHE 0.007 0.001 PHE A 841 TYR 0.013 0.001 TYR A 691 ARG 0.002 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8275 (p90) cc_final: 0.8071 (p90) REVERT: A 444 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7641 (mtmm) REVERT: A 469 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7958 (mmm160) outliers start: 12 outliers final: 11 residues processed: 53 average time/residue: 0.2057 time to fit residues: 14.8499 Evaluate side-chains 54 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 TYR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.091250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061134 restraints weight = 19429.064| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.58 r_work: 0.2970 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6533 Z= 0.273 Angle : 0.607 7.826 8876 Z= 0.298 Chirality : 0.041 0.189 1039 Planarity : 0.004 0.044 1118 Dihedral : 6.656 127.323 888 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.61 % Allowed : 15.20 % Favored : 83.19 % 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: 0.41 (0.31), residues: 823 helix: 2.17 (0.26), residues: 444 sheet: -1.85 (0.62), residues: 58 loop : -2.19 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 846 HIS 0.014 0.001 HIS A 701 PHE 0.011 0.001 PHE A 705 TYR 0.013 0.001 TYR A 691 ARG 0.001 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8289 (p90) cc_final: 0.8068 (p90) REVERT: A 469 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7936 (mmm160) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.2100 time to fit residues: 13.7841 Evaluate side-chains 51 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 TYR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 846 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.090991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060122 restraints weight = 19609.821| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.46 r_work: 0.3018 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6533 Z= 0.215 Angle : 0.585 7.644 8876 Z= 0.286 Chirality : 0.041 0.193 1039 Planarity : 0.003 0.043 1118 Dihedral : 6.575 130.461 888 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.75 % Allowed : 14.91 % Favored : 83.33 % 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: 0.42 (0.31), residues: 823 helix: 2.16 (0.26), residues: 444 sheet: -1.86 (0.62), residues: 58 loop : -2.15 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 846 HIS 0.014 0.001 HIS A 701 PHE 0.008 0.001 PHE A 841 TYR 0.013 0.001 TYR A 691 ARG 0.001 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3627.38 seconds wall clock time: 65 minutes 37.07 seconds (3937.07 seconds total)