Starting phenix.real_space_refine on Tue Feb 3 15:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9km4_62422/02_2026/9km4_62422.cif Found real_map, /net/cci-nas-00/data/ceres_data/9km4_62422/02_2026/9km4_62422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9km4_62422/02_2026/9km4_62422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9km4_62422/02_2026/9km4_62422.map" model { file = "/net/cci-nas-00/data/ceres_data/9km4_62422/02_2026/9km4_62422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9km4_62422/02_2026/9km4_62422.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 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 36 5.16 5 C 2980 2.51 5 N 667 2.21 5 O 741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4424 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4363 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 30, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Unusual residues: {'CLR': 1, 'OLA': 1} Inner-chain residues flagged as termini: ['pdbres="DLY A 802 "'] Classifications: {'peptide': 1, 'undetermined': 2, 'water': 4} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.12, per 1000 atoms: 0.25 Number of scatterers: 4424 At special positions: 0 Unit cell: (79.05, 69.7, 87.55, 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 36 16.00 O 741 8.00 N 667 7.00 C 2980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 312 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 307.7 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DLY A 802 " Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 77.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.591A pdb=" N PHE A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.962A pdb=" N TRP A 207 " --> pdb=" O GLY A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 248 removed outlier: 5.168A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.756A pdb=" N ALA A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.597A pdb=" N TRP A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 256 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 257 " --> pdb=" O VAL A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 262 through 293 removed outlier: 3.759A pdb=" N ILE A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 4.010A pdb=" N SER A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 385 through 402 Processing helix chain 'A' and resid 406 through 418 removed outlier: 4.806A pdb=" N LYS A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.914A pdb=" N THR A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.817A pdb=" N TRP A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.718A pdb=" N THR A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 520 removed outlier: 3.651A pdb=" N ASP A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 541 through 547 removed outlier: 3.576A pdb=" N ALA A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 586 removed outlier: 3.858A pdb=" N TRP A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 616 through 628 removed outlier: 4.065A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 647 removed outlier: 3.567A pdb=" N ILE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 676 through 691 removed outlier: 5.409A pdb=" N THR A 682 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 719 removed outlier: 3.672A pdb=" N MET A 709 " --> pdb=" O TRP A 705 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.572A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 743 Processing helix chain 'A' and resid 754 through 758 Processing sheet with id=AA1, first strand: chain 'A' and resid 696 through 697 248 hydrogen bonds defined for protein. 720 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: 0.71 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 646 1.31 - 1.44: 1351 1.44 - 1.56: 2506 1.56 - 1.69: 2 1.69 - 1.81: 59 Bond restraints: 4564 Sorted by residual: bond pdb=" C PRO A 448 " pdb=" O PRO A 448 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C ILE A 466 " pdb=" O ILE A 466 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.19e-02 7.06e+03 1.40e+01 bond pdb=" N THR A 464 " pdb=" CA THR A 464 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.20e-02 6.94e+03 1.09e+01 bond pdb=" N PHE A 468 " pdb=" CA PHE A 468 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.33e-02 5.65e+03 9.79e+00 bond pdb=" N TRP A 450 " pdb=" CA TRP A 450 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.40e+00 ... (remaining 4559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 6136 3.16 - 6.32: 64 6.32 - 9.49: 8 9.49 - 12.65: 9 12.65 - 15.81: 2 Bond angle restraints: 6219 Sorted by residual: angle pdb=" C12 CLR A 801 " pdb=" C13 CLR A 801 " pdb=" C17 CLR A 801 " ideal model delta sigma weight residual 116.52 100.71 15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" C14 CLR A 801 " pdb=" C13 CLR A 801 " pdb=" C18 CLR A 801 " ideal model delta sigma weight residual 112.24 127.63 -15.39 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C PHE A 467 " pdb=" CA PHE A 467 " pdb=" CB PHE A 467 " ideal model delta sigma weight residual 110.38 100.28 10.10 2.04e+00 2.40e-01 2.45e+01 angle pdb=" CA PHE A 467 " pdb=" CB PHE A 467 " pdb=" CG PHE A 467 " ideal model delta sigma weight residual 113.80 118.37 -4.57 1.00e+00 1.00e+00 2.08e+01 angle pdb=" C ALA A 456 " pdb=" N MET A 457 " pdb=" CA MET A 457 " ideal model delta sigma weight residual 120.79 114.49 6.30 1.39e+00 5.18e-01 2.06e+01 ... (remaining 6214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 2375 22.21 - 44.41: 227 44.41 - 66.62: 48 66.62 - 88.82: 5 88.82 - 111.03: 4 Dihedral angle restraints: 2659 sinusoidal: 1069 harmonic: 1590 Sorted by residual: dihedral pdb=" C PHE A 467 " pdb=" N PHE A 467 " pdb=" CA PHE A 467 " pdb=" CB PHE A 467 " ideal model delta harmonic sigma weight residual -122.60 -110.53 -12.07 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" CA PRO A 678 " pdb=" C PRO A 678 " pdb=" N THR A 679 " pdb=" CA THR A 679 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C1 CLR A 801 " pdb=" C2 CLR A 801 " pdb=" C3 CLR A 801 " pdb=" O1 CLR A 801 " ideal model delta sinusoidal sigma weight residual 180.04 69.01 111.03 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 2656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 676 0.110 - 0.220: 10 0.220 - 0.329: 3 0.329 - 0.439: 1 0.439 - 0.549: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" C20 CLR A 801 " pdb=" C17 CLR A 801 " pdb=" C21 CLR A 801 " pdb=" C22 CLR A 801 " both_signs ideal model delta sigma weight residual False 2.59 2.04 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" C9 CLR A 801 " pdb=" C10 CLR A 801 " pdb=" C11 CLR A 801 " pdb=" C8 CLR A 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.80 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA LYS A 449 " pdb=" N LYS A 449 " pdb=" C LYS A 449 " pdb=" CB LYS A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 688 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 435 " -0.063 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A 436 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 456 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ALA A 456 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA A 456 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 457 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 463 " -0.010 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ALA A 463 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA A 463 " -0.011 2.00e-02 2.50e+03 pdb=" N THR A 464 " -0.011 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 415 2.74 - 3.28: 4261 3.28 - 3.82: 7194 3.82 - 4.36: 8073 4.36 - 4.90: 14798 Nonbonded interactions: 34741 Sorted by model distance: nonbonded pdb=" OG1 THR A 309 " pdb=" OD1 ASP A 311 " model vdw 2.204 3.040 nonbonded pdb=" O PHE A 510 " pdb=" OG SER A 514 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR A 417 " pdb=" OD1 ASP A 569 " model vdw 2.293 3.040 nonbonded pdb=" O PRO A 703 " pdb=" OG SER A 706 " model vdw 2.330 3.040 nonbonded pdb=" O ALA A 732 " pdb=" NE ARG A 739 " model vdw 2.406 3.120 ... (remaining 34736 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.004 0.095 4566 Z= 0.272 Angle : 0.865 15.812 6221 Z= 0.426 Chirality : 0.052 0.549 691 Planarity : 0.005 0.094 747 Dihedral : 17.762 111.026 1640 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 0.64 % Allowed : 20.39 % Favored : 78.97 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.37), residues: 544 helix: 1.12 (0.29), residues: 342 sheet: None (None), residues: 0 loop : -0.23 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.017 0.001 TYR A 690 PHE 0.015 0.001 PHE A 467 TRP 0.030 0.001 TRP A 750 HIS 0.001 0.000 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 4564) covalent geometry : angle 0.86482 ( 6219) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.56647 ( 2) hydrogen bonds : bond 0.20648 ( 248) hydrogen bonds : angle 6.19940 ( 720) Misc. bond : bond 0.09454 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.174 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 0.0596 time to fit residues: 5.2105 Evaluate side-chains 64 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.181529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152668 restraints weight = 5589.595| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.23 r_work: 0.3658 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4566 Z= 0.127 Angle : 0.546 8.649 6221 Z= 0.276 Chirality : 0.041 0.129 691 Planarity : 0.005 0.059 747 Dihedral : 9.924 74.176 673 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.93 % Allowed : 21.24 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.38), residues: 544 helix: 1.48 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -0.30 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.018 0.001 TYR A 278 PHE 0.009 0.001 PHE A 725 TRP 0.009 0.001 TRP A 750 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4564) covalent geometry : angle 0.54620 ( 6219) SS BOND : bond 0.00237 ( 1) SS BOND : angle 0.87082 ( 2) hydrogen bonds : bond 0.04564 ( 248) hydrogen bonds : angle 4.24433 ( 720) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.110 Fit side-chains REVERT: A 360 VAL cc_start: 0.6788 (t) cc_final: 0.6572 (p) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.0433 time to fit residues: 4.0865 Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 644 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.181891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152758 restraints weight = 5500.109| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.29 r_work: 0.3657 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4566 Z= 0.111 Angle : 0.490 6.477 6221 Z= 0.251 Chirality : 0.040 0.128 691 Planarity : 0.005 0.056 747 Dihedral : 7.056 68.482 673 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 21.03 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.38), residues: 544 helix: 1.82 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.29 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 739 TYR 0.016 0.001 TYR A 278 PHE 0.006 0.001 PHE A 559 TRP 0.006 0.001 TRP A 750 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4564) covalent geometry : angle 0.48995 ( 6219) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.71550 ( 2) hydrogen bonds : bond 0.04104 ( 248) hydrogen bonds : angle 4.06587 ( 720) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.155 Fit side-chains REVERT: A 360 VAL cc_start: 0.6799 (t) cc_final: 0.6593 (p) REVERT: A 667 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5961 (ppt170) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.0626 time to fit residues: 5.7288 Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 667 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 14 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 0.0170 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157152 restraints weight = 5474.845| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.24 r_work: 0.3712 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4566 Z= 0.094 Angle : 0.461 5.943 6221 Z= 0.236 Chirality : 0.039 0.121 691 Planarity : 0.005 0.053 747 Dihedral : 6.376 67.277 673 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 20.39 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.38), residues: 544 helix: 1.88 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 761 TYR 0.014 0.001 TYR A 278 PHE 0.006 0.001 PHE A 725 TRP 0.005 0.001 TRP A 705 HIS 0.001 0.000 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 4564) covalent geometry : angle 0.46058 ( 6219) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.48117 ( 2) hydrogen bonds : bond 0.03253 ( 248) hydrogen bonds : angle 3.88528 ( 720) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.169 Fit side-chains REVERT: A 454 MET cc_start: 0.7650 (ptm) cc_final: 0.6046 (mmt) REVERT: A 667 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.5875 (ppt170) outliers start: 14 outliers final: 3 residues processed: 71 average time/residue: 0.0458 time to fit residues: 4.3892 Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 667 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.181304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152183 restraints weight = 5529.595| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.24 r_work: 0.3654 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4566 Z= 0.118 Angle : 0.494 6.407 6221 Z= 0.253 Chirality : 0.040 0.133 691 Planarity : 0.005 0.053 747 Dihedral : 6.003 64.859 672 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.15 % Allowed : 21.24 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.37), residues: 544 helix: 1.98 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.36 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 739 TYR 0.018 0.001 TYR A 278 PHE 0.007 0.001 PHE A 663 TRP 0.010 0.001 TRP A 186 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4564) covalent geometry : angle 0.49375 ( 6219) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.41152 ( 2) hydrogen bonds : bond 0.04101 ( 248) hydrogen bonds : angle 3.98318 ( 720) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.149 Fit side-chains REVERT: A 454 MET cc_start: 0.7497 (ptm) cc_final: 0.6053 (mmt) REVERT: A 667 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5790 (ppt170) outliers start: 10 outliers final: 4 residues processed: 66 average time/residue: 0.0583 time to fit residues: 5.0849 Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 679 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.181121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152822 restraints weight = 5677.210| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.21 r_work: 0.3677 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4566 Z= 0.101 Angle : 0.478 6.112 6221 Z= 0.243 Chirality : 0.039 0.124 691 Planarity : 0.005 0.052 747 Dihedral : 5.763 64.039 672 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 21.67 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.37), residues: 544 helix: 2.07 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.34 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 739 TYR 0.016 0.001 TYR A 278 PHE 0.005 0.001 PHE A 559 TRP 0.007 0.001 TRP A 186 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 4564) covalent geometry : angle 0.47757 ( 6219) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.51884 ( 2) hydrogen bonds : bond 0.03598 ( 248) hydrogen bonds : angle 3.93580 ( 720) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.150 Fit side-chains REVERT: A 454 MET cc_start: 0.7415 (ptm) cc_final: 0.6461 (mmt) REVERT: A 667 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5809 (ppt170) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.0590 time to fit residues: 5.0693 Evaluate side-chains 63 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 679 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.180108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151348 restraints weight = 5614.546| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.23 r_work: 0.3658 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4566 Z= 0.110 Angle : 0.489 6.649 6221 Z= 0.248 Chirality : 0.040 0.129 691 Planarity : 0.005 0.049 747 Dihedral : 5.653 61.611 672 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.93 % Allowed : 21.67 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.37), residues: 544 helix: 1.90 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -0.41 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 739 TYR 0.017 0.001 TYR A 278 PHE 0.006 0.001 PHE A 559 TRP 0.006 0.001 TRP A 186 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4564) covalent geometry : angle 0.48899 ( 6219) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.61513 ( 2) hydrogen bonds : bond 0.03869 ( 248) hydrogen bonds : angle 3.96014 ( 720) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.157 Fit side-chains REVERT: A 454 MET cc_start: 0.7342 (ptm) cc_final: 0.6474 (mmt) REVERT: A 667 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5784 (ppt170) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.0621 time to fit residues: 5.3272 Evaluate side-chains 64 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 679 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.180240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151657 restraints weight = 5583.193| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.23 r_work: 0.3661 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4566 Z= 0.105 Angle : 0.486 6.150 6221 Z= 0.249 Chirality : 0.040 0.127 691 Planarity : 0.005 0.051 747 Dihedral : 5.596 60.570 672 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 21.03 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.37), residues: 544 helix: 1.95 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -0.41 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 739 TYR 0.016 0.001 TYR A 278 PHE 0.006 0.001 PHE A 559 TRP 0.006 0.001 TRP A 186 HIS 0.001 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4564) covalent geometry : angle 0.48620 ( 6219) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.57969 ( 2) hydrogen bonds : bond 0.03664 ( 248) hydrogen bonds : angle 3.93928 ( 720) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.095 Fit side-chains REVERT: A 407 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7261 (tp) REVERT: A 454 MET cc_start: 0.7254 (ptm) cc_final: 0.6475 (mmt) REVERT: A 667 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.5779 (ppt170) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.0561 time to fit residues: 4.9642 Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 717 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.180326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151738 restraints weight = 5542.151| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.22 r_work: 0.3664 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4566 Z= 0.105 Angle : 0.479 6.108 6221 Z= 0.245 Chirality : 0.040 0.128 691 Planarity : 0.005 0.050 747 Dihedral : 5.534 59.397 672 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.15 % Allowed : 20.82 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.37), residues: 544 helix: 1.94 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -0.39 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 758 TYR 0.016 0.001 TYR A 278 PHE 0.006 0.001 PHE A 559 TRP 0.006 0.001 TRP A 186 HIS 0.003 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4564) covalent geometry : angle 0.47940 ( 6219) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.61200 ( 2) hydrogen bonds : bond 0.03686 ( 248) hydrogen bonds : angle 3.93539 ( 720) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.208 Fit side-chains REVERT: A 407 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7262 (tp) REVERT: A 454 MET cc_start: 0.7206 (ptm) cc_final: 0.6494 (mmt) REVERT: A 667 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.5766 (ppt170) REVERT: A 690 TYR cc_start: 0.6409 (t80) cc_final: 0.6115 (t80) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.0613 time to fit residues: 5.3964 Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 717 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.181267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152795 restraints weight = 5562.541| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.20 r_work: 0.3679 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4566 Z= 0.099 Angle : 0.475 5.929 6221 Z= 0.242 Chirality : 0.039 0.127 691 Planarity : 0.005 0.050 747 Dihedral : 5.324 57.524 672 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.93 % Allowed : 21.46 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.37), residues: 544 helix: 1.98 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -0.45 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.015 0.001 TYR A 278 PHE 0.005 0.001 PHE A 559 TRP 0.006 0.001 TRP A 186 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 4564) covalent geometry : angle 0.47456 ( 6219) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.55586 ( 2) hydrogen bonds : bond 0.03450 ( 248) hydrogen bonds : angle 3.89870 ( 720) Misc. bond : bond 0.00002 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.158 Fit side-chains REVERT: A 407 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7218 (tp) REVERT: A 454 MET cc_start: 0.7142 (ptm) cc_final: 0.6497 (mmt) REVERT: A 667 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5740 (ppt170) REVERT: A 690 TYR cc_start: 0.6401 (t80) cc_final: 0.6104 (t80) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.0571 time to fit residues: 4.6435 Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 667 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 51 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.182357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153888 restraints weight = 5613.979| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.22 r_work: 0.3691 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4566 Z= 0.095 Angle : 0.466 5.765 6221 Z= 0.237 Chirality : 0.039 0.127 691 Planarity : 0.004 0.048 747 Dihedral : 5.026 54.205 672 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.50 % Allowed : 21.89 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.37), residues: 544 helix: 2.01 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -0.43 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.015 0.001 TYR A 278 PHE 0.006 0.001 PHE A 610 TRP 0.005 0.001 TRP A 186 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4564) covalent geometry : angle 0.46560 ( 6219) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.58077 ( 2) hydrogen bonds : bond 0.03309 ( 248) hydrogen bonds : angle 3.86229 ( 720) Misc. bond : bond 0.00000 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1021.29 seconds wall clock time: 18 minutes 13.19 seconds (1093.19 seconds total)