Starting phenix.real_space_refine on Mon Mar 11 01:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhu_36294/03_2024/8jhu_36294.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhu_36294/03_2024/8jhu_36294.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhu_36294/03_2024/8jhu_36294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhu_36294/03_2024/8jhu_36294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhu_36294/03_2024/8jhu_36294.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhu_36294/03_2024/8jhu_36294.pdb" } 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= 0.005 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 4159 2.51 5 N 1117 2.21 5 O 1262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6554 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6554 Classifications: {'peptide': 811} Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 774} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 709 " occ=0.61 ... (7 atoms not shown) pdb=" OE2 GLU A 709 " occ=0.61 Time building chain proxies: 3.80, per 1000 atoms: 0.58 Number of scatterers: 6554 At special positions: 0 Unit cell: (85.244, 114.784, 78.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1262 8.00 N 1117 7.00 C 4159 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 - 3.50 Amino acid : False - 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 3 sheets defined 53.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 17 through 34 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 136 through 166 removed outlier: 4.937A pdb=" N ALA A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.642A pdb=" N ALA A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.626A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 225 removed outlier: 3.516A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 272 through 294 removed outlier: 3.664A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.730A pdb=" N VAL A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 410 through 424 Processing helix chain 'A' and resid 427 through 439 removed outlier: 4.201A pdb=" N VAL A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.541A pdb=" N ALA A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.570A pdb=" N THR A 488 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 503 removed outlier: 3.902A pdb=" N GLN A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.503A pdb=" N ALA A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 4.111A pdb=" N ALA A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 615 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.733A pdb=" N GLU A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 removed outlier: 3.526A pdb=" N LYS A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.881A pdb=" N TRP A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 677 " --> pdb=" O ARG A 673 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASN A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 732 through 737 removed outlier: 3.599A pdb=" N ILE A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 776 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 805 through 809 removed outlier: 3.707A pdb=" N GLN A 809 " --> pdb=" O TYR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 839 through 854 Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 870 through 874 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.790A pdb=" N ILE A 4 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU A 42 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 6 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS A 3 " --> pdb=" O HIS A 447 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP A 449 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A 5 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS A 451 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 7 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR A 446 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN A 477 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 448 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 479 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 450 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.698A pdb=" N SER A 82 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL A 113 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 84 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 699 through 703 removed outlier: 3.772A pdb=" N GLY A 633 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 590 " --> pdb=" O LYS A 630 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA A 632 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER A 592 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 591 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 720 " --> pdb=" O TYR A 745 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 744 " --> pdb=" O ASP A 767 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 798 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: 1.97 Time building geometry restraints manager: 2.58 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: 1363 1.33 - 1.45: 1417 1.45 - 1.57: 3872 1.57 - 1.69: 1 1.69 - 1.81: 24 Bond restraints: 6677 Sorted by residual: bond pdb=" CE1 HIS A 661 " pdb=" NE2 HIS A 661 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.67e+01 bond pdb=" N VAL A 693 " pdb=" CA VAL A 693 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 8.09e+00 bond pdb=" CB PRO A 815 " pdb=" CG PRO A 815 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.24e+00 bond pdb=" CA ALA A 692 " pdb=" CB ALA A 692 " ideal model delta sigma weight residual 1.535 1.493 0.042 1.71e-02 3.42e+03 6.02e+00 bond pdb=" N LYS A 659 " pdb=" CA LYS A 659 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.84e+00 ... (remaining 6672 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.95: 110 104.95 - 112.21: 3296 112.21 - 119.46: 2324 119.46 - 126.72: 3206 126.72 - 133.97: 68 Bond angle restraints: 9004 Sorted by residual: angle pdb=" CA PRO A 815 " pdb=" N PRO A 815 " pdb=" CD PRO A 815 " ideal model delta sigma weight residual 112.00 101.70 10.30 1.40e+00 5.10e-01 5.41e+01 angle pdb=" N GLU A 689 " pdb=" CA GLU A 689 " pdb=" C GLU A 689 " ideal model delta sigma weight residual 110.80 98.62 12.18 2.13e+00 2.20e-01 3.27e+01 angle pdb=" N ASN A 695 " pdb=" CA ASN A 695 " pdb=" C ASN A 695 " ideal model delta sigma weight residual 110.28 102.31 7.97 1.48e+00 4.57e-01 2.90e+01 angle pdb=" N SER A 670 " pdb=" CA SER A 670 " pdb=" C SER A 670 " ideal model delta sigma weight residual 114.75 107.98 6.77 1.26e+00 6.30e-01 2.89e+01 angle pdb=" N PRO A 662 " pdb=" CA PRO A 662 " pdb=" C PRO A 662 " ideal model delta sigma weight residual 110.40 116.85 -6.45 1.61e+00 3.86e-01 1.61e+01 ... (remaining 8999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3636 17.96 - 35.91: 386 35.91 - 53.87: 87 53.87 - 71.83: 18 71.83 - 89.79: 6 Dihedral angle restraints: 4133 sinusoidal: 1738 harmonic: 2395 Sorted by residual: dihedral pdb=" CA ALA A 685 " pdb=" C ALA A 685 " pdb=" N LYS A 686 " pdb=" CA LYS A 686 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP A 674 " pdb=" C ASP A 674 " pdb=" N TYR A 675 " pdb=" CA TYR A 675 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB GLU A 62 " pdb=" CG GLU A 62 " pdb=" CD GLU A 62 " pdb=" OE1 GLU A 62 " ideal model delta sinusoidal sigma weight residual 0.00 -89.79 89.79 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 806 0.049 - 0.098: 151 0.098 - 0.147: 31 0.147 - 0.197: 3 0.197 - 0.246: 2 Chirality restraints: 993 Sorted by residual: chirality pdb=" CA LEU A 694 " pdb=" N LEU A 694 " pdb=" C LEU A 694 " pdb=" CB LEU A 694 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA PRO A 662 " pdb=" N PRO A 662 " pdb=" C PRO A 662 " pdb=" CB PRO A 662 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA TYR A 663 " pdb=" N TYR A 663 " pdb=" C TYR A 663 " pdb=" CB TYR A 663 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 990 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 688 " -0.028 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C LYS A 688 " 0.099 2.00e-02 2.50e+03 pdb=" O LYS A 688 " -0.037 2.00e-02 2.50e+03 pdb=" N GLU A 689 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 814 " 0.088 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO A 815 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO A 815 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 815 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 695 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ASN A 695 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN A 695 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 696 " 0.018 2.00e-02 2.50e+03 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 482 2.74 - 3.28: 6620 3.28 - 3.82: 11187 3.82 - 4.36: 13620 4.36 - 4.90: 23081 Nonbonded interactions: 54990 Sorted by model distance: nonbonded pdb=" OD2 ASP A 12 " pdb=" OG1 THR A 17 " model vdw 2.200 2.440 nonbonded pdb=" OG SER A 67 " pdb=" OD2 ASP A 425 " model vdw 2.243 2.440 nonbonded pdb=" OG SER A 59 " pdb=" O PRO A 61 " model vdw 2.278 2.440 nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 108 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR A 745 " pdb=" OG SER A 821 " model vdw 2.282 2.440 ... (remaining 54985 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=0.61 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: 1.160 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: 3.810 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.820 Find NCS groups from input model: 0.170 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 6677 Z= 0.212 Angle : 0.589 12.178 9004 Z= 0.344 Chirality : 0.042 0.246 993 Planarity : 0.005 0.126 1165 Dihedral : 15.641 89.785 2583 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.35 % Favored : 94.15 % Rotamer: Outliers : 0.82 % Allowed : 18.52 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.27 (0.31), residues: 803 helix: 1.40 (0.28), residues: 381 sheet: -1.28 (0.56), residues: 81 loop : -1.77 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 41 HIS 0.005 0.001 HIS A 661 PHE 0.008 0.001 PHE A 219 TYR 0.009 0.001 TYR A 495 ARG 0.006 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.707 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.1896 time to fit residues: 20.3810 Evaluate side-chains 78 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6677 Z= 0.182 Angle : 0.472 7.171 9004 Z= 0.246 Chirality : 0.039 0.130 993 Planarity : 0.004 0.071 1165 Dihedral : 4.692 59.509 886 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.37 % Allowed : 18.11 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.05 (0.31), residues: 803 helix: 1.63 (0.28), residues: 387 sheet: -1.57 (0.53), residues: 87 loop : -1.68 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 41 HIS 0.002 0.001 HIS A 579 PHE 0.011 0.001 PHE A 415 TYR 0.009 0.001 TYR A 491 ARG 0.005 0.000 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.761 Fit side-chains REVERT: A 607 LYS cc_start: 0.8025 (tppp) cc_final: 0.7403 (tppt) REVERT: A 614 ASP cc_start: 0.7835 (m-30) cc_final: 0.7451 (m-30) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.1650 time to fit residues: 19.2212 Evaluate side-chains 71 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 593 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6677 Z= 0.273 Angle : 0.518 7.025 9004 Z= 0.270 Chirality : 0.041 0.130 993 Planarity : 0.004 0.055 1165 Dihedral : 4.081 17.765 876 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.33 % Allowed : 18.24 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.19 (0.30), residues: 803 helix: 1.47 (0.27), residues: 388 sheet: -1.65 (0.57), residues: 77 loop : -1.70 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 41 HIS 0.003 0.001 HIS A 416 PHE 0.016 0.002 PHE A 219 TYR 0.011 0.001 TYR A 491 ARG 0.004 0.001 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.809 Fit side-chains REVERT: A 356 ASN cc_start: 0.7977 (t0) cc_final: 0.7494 (t0) REVERT: A 404 TYR cc_start: 0.8841 (m-80) cc_final: 0.8392 (m-80) REVERT: A 513 ASP cc_start: 0.7964 (p0) cc_final: 0.7713 (p0) REVERT: A 607 LYS cc_start: 0.8112 (tppp) cc_final: 0.7652 (tptt) REVERT: A 681 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7112 (ttp80) REVERT: A 711 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6254 (tp) REVERT: A 839 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.4458 (m-30) outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 0.1785 time to fit residues: 21.2951 Evaluate side-chains 81 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6677 Z= 0.175 Angle : 0.462 8.016 9004 Z= 0.240 Chirality : 0.039 0.136 993 Planarity : 0.004 0.048 1165 Dihedral : 3.939 17.027 876 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.47 % Allowed : 18.24 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.04 (0.31), residues: 803 helix: 1.63 (0.27), residues: 390 sheet: -1.67 (0.57), residues: 77 loop : -1.67 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.001 0.000 HIS A 202 PHE 0.009 0.001 PHE A 219 TYR 0.010 0.001 TYR A 259 ARG 0.002 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.705 Fit side-chains REVERT: A 356 ASN cc_start: 0.7988 (t0) cc_final: 0.7490 (t0) REVERT: A 513 ASP cc_start: 0.7921 (p0) cc_final: 0.7623 (p0) REVERT: A 607 LYS cc_start: 0.8090 (tppp) cc_final: 0.7627 (tptt) REVERT: A 681 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7148 (ttp80) REVERT: A 711 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6273 (tp) REVERT: A 839 ASP cc_start: 0.5567 (OUTLIER) cc_final: 0.4458 (m-30) outliers start: 18 outliers final: 10 residues processed: 92 average time/residue: 0.1695 time to fit residues: 21.8031 Evaluate side-chains 87 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6677 Z= 0.180 Angle : 0.465 8.875 9004 Z= 0.240 Chirality : 0.039 0.132 993 Planarity : 0.004 0.048 1165 Dihedral : 3.936 17.170 876 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.47 % Allowed : 18.11 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.05 (0.31), residues: 803 helix: 1.73 (0.27), residues: 389 sheet: -1.74 (0.56), residues: 77 loop : -1.62 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.001 0.000 HIS A 708 PHE 0.011 0.001 PHE A 219 TYR 0.011 0.001 TYR A 177 ARG 0.003 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.736 Fit side-chains REVERT: A 356 ASN cc_start: 0.7983 (t0) cc_final: 0.7463 (t0) REVERT: A 398 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8029 (mt-10) REVERT: A 433 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: A 513 ASP cc_start: 0.7925 (p0) cc_final: 0.7658 (p0) REVERT: A 607 LYS cc_start: 0.8052 (tppp) cc_final: 0.7614 (tptt) REVERT: A 681 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7199 (ttp80) REVERT: A 711 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6312 (tp) REVERT: A 839 ASP cc_start: 0.5494 (OUTLIER) cc_final: 0.4486 (t0) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.1638 time to fit residues: 20.6888 Evaluate side-chains 87 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6677 Z= 0.181 Angle : 0.468 9.749 9004 Z= 0.242 Chirality : 0.039 0.133 993 Planarity : 0.004 0.049 1165 Dihedral : 3.949 17.104 876 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.74 % Allowed : 18.79 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.13 (0.31), residues: 803 helix: 1.83 (0.27), residues: 388 sheet: -1.82 (0.56), residues: 77 loop : -1.57 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.000 HIS A 202 PHE 0.011 0.001 PHE A 219 TYR 0.010 0.001 TYR A 495 ARG 0.004 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.789 Fit side-chains REVERT: A 356 ASN cc_start: 0.7944 (t0) cc_final: 0.7413 (t0) REVERT: A 433 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: A 513 ASP cc_start: 0.7945 (p0) cc_final: 0.7655 (p0) REVERT: A 607 LYS cc_start: 0.8068 (tppp) cc_final: 0.7656 (tptt) REVERT: A 681 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7247 (ttp80) REVERT: A 711 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6330 (tp) REVERT: A 839 ASP cc_start: 0.5633 (OUTLIER) cc_final: 0.4495 (m-30) outliers start: 20 outliers final: 12 residues processed: 95 average time/residue: 0.1631 time to fit residues: 22.1448 Evaluate side-chains 87 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6677 Z= 0.181 Angle : 0.478 10.210 9004 Z= 0.244 Chirality : 0.039 0.131 993 Planarity : 0.004 0.050 1165 Dihedral : 3.949 17.063 876 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.19 % Allowed : 20.03 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.31), residues: 803 helix: 1.87 (0.27), residues: 388 sheet: -1.84 (0.56), residues: 77 loop : -1.56 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.000 HIS A 202 PHE 0.012 0.001 PHE A 219 TYR 0.010 0.001 TYR A 495 ARG 0.003 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.826 Fit side-chains REVERT: A 356 ASN cc_start: 0.7946 (t0) cc_final: 0.7404 (t0) REVERT: A 398 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8027 (mt-10) REVERT: A 433 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: A 513 ASP cc_start: 0.7956 (p0) cc_final: 0.7672 (p0) REVERT: A 607 LYS cc_start: 0.8067 (tppp) cc_final: 0.7659 (tptt) REVERT: A 636 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: A 681 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7267 (ttp80) REVERT: A 711 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6407 (tp) REVERT: A 839 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.4439 (m-30) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.1676 time to fit residues: 20.2119 Evaluate side-chains 89 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6677 Z= 0.164 Angle : 0.468 9.372 9004 Z= 0.240 Chirality : 0.039 0.132 993 Planarity : 0.004 0.048 1165 Dihedral : 3.909 16.932 876 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.47 % Allowed : 20.03 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.23 (0.31), residues: 803 helix: 1.93 (0.27), residues: 389 sheet: -1.87 (0.57), residues: 76 loop : -1.54 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.000 HIS A 202 PHE 0.010 0.001 PHE A 219 TYR 0.010 0.001 TYR A 495 ARG 0.002 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.780 Fit side-chains REVERT: A 356 ASN cc_start: 0.7942 (t0) cc_final: 0.7399 (t0) REVERT: A 398 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8029 (mt-10) REVERT: A 433 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: A 513 ASP cc_start: 0.7942 (p0) cc_final: 0.7647 (p0) REVERT: A 636 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: A 711 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6413 (tp) REVERT: A 839 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.4402 (m-30) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.1904 time to fit residues: 23.9264 Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6677 Z= 0.155 Angle : 0.463 9.089 9004 Z= 0.238 Chirality : 0.039 0.132 993 Planarity : 0.004 0.049 1165 Dihedral : 3.844 16.871 876 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.33 % Allowed : 20.16 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.32 (0.31), residues: 803 helix: 2.01 (0.28), residues: 389 sheet: -1.80 (0.57), residues: 76 loop : -1.51 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.000 HIS A 202 PHE 0.009 0.001 PHE A 219 TYR 0.010 0.001 TYR A 495 ARG 0.004 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.380 Fit side-chains REVERT: A 356 ASN cc_start: 0.7938 (t0) cc_final: 0.7393 (t0) REVERT: A 398 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8019 (mt-10) REVERT: A 433 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: A 513 ASP cc_start: 0.7922 (p0) cc_final: 0.7647 (p0) REVERT: A 607 LYS cc_start: 0.8190 (tppp) cc_final: 0.7604 (tppt) REVERT: A 636 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: A 711 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6403 (tp) REVERT: A 839 ASP cc_start: 0.5478 (OUTLIER) cc_final: 0.4455 (m-30) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 0.2083 time to fit residues: 26.3391 Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6677 Z= 0.188 Angle : 0.486 11.082 9004 Z= 0.249 Chirality : 0.039 0.132 993 Planarity : 0.004 0.049 1165 Dihedral : 3.946 16.977 876 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.19 % Allowed : 20.99 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.29 (0.31), residues: 803 helix: 1.98 (0.27), residues: 388 sheet: -1.99 (0.56), residues: 75 loop : -1.46 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.000 HIS A 202 PHE 0.012 0.001 PHE A 219 TYR 0.010 0.001 TYR A 495 ARG 0.004 0.000 ARG A 681 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.873 Fit side-chains REVERT: A 356 ASN cc_start: 0.7946 (t0) cc_final: 0.7390 (t0) REVERT: A 398 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8016 (mt-10) REVERT: A 433 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: A 513 ASP cc_start: 0.7949 (p0) cc_final: 0.7667 (p0) REVERT: A 607 LYS cc_start: 0.8218 (tppp) cc_final: 0.7632 (tppt) REVERT: A 711 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6419 (tp) REVERT: A 839 ASP cc_start: 0.5519 (OUTLIER) cc_final: 0.4502 (m-30) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 0.1745 time to fit residues: 21.6904 Evaluate side-chains 90 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 839 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.101128 restraints weight = 7490.951| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.82 r_work: 0.3244 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6677 Z= 0.353 Angle : 0.591 10.909 9004 Z= 0.305 Chirality : 0.043 0.152 993 Planarity : 0.005 0.049 1165 Dihedral : 4.554 19.141 876 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.33 % Allowed : 20.85 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.15 (0.31), residues: 803 helix: 1.61 (0.27), residues: 392 sheet: -2.49 (0.54), residues: 76 loop : -1.62 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 41 HIS 0.003 0.001 HIS A 872 PHE 0.023 0.002 PHE A 219 TYR 0.010 0.002 TYR A 491 ARG 0.004 0.001 ARG A 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.90 seconds wall clock time: 32 minutes 7.76 seconds (1927.76 seconds total)