Starting phenix.real_space_refine on Thu Jul 2 04:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.map" model { file = "/net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wxi_32880/07_2026/7wxi_32880.cif" } resolution = 4.2 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= 0.004 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 4064 2.51 5 N 1174 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6522 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Restraints were copied for chains: B Time building chain proxies: 1.85, per 1000 atoms: 0.28 Number of scatterers: 6522 At special positions: 0 Unit cell: (98.58, 92.22, 62.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 1252 8.00 N 1174 7.00 C 4064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 442.8 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP A 801 " pdb=" CB RGP B 801 " Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 50.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 348 through 364 removed outlier: 4.096A pdb=" N ALA A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.777A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 495 through 513 removed outlier: 4.331A pdb=" N VAL A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.772A pdb=" N ALA A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.626A pdb=" N ALA A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 removed outlier: 3.628A pdb=" N ALA A 714 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 348 through 364 removed outlier: 4.096A pdb=" N ALA B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.777A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 495 through 513 removed outlier: 4.331A pdb=" N VAL B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.772A pdb=" N ALA B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.626A pdb=" N ALA B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 removed outlier: 3.628A pdb=" N ALA B 714 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 751 removed outlier: 4.420A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 771 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.555A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 607 removed outlier: 5.647A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.895A pdb=" N LYS A 629 " --> pdb=" O CYS A 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA7, first strand: chain 'B' and resid 750 through 751 removed outlier: 4.420A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 771 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 457 Processing sheet with id=AA9, first strand: chain 'B' and resid 487 through 490 removed outlier: 6.555A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 605 through 607 removed outlier: 5.647A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 629 through 630 removed outlier: 6.895A pdb=" N LYS B 629 " --> pdb=" O CYS B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 727 through 728 300 hydrogen bonds defined for protein. 822 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: 0.95 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1140 1.31 - 1.43: 1536 1.43 - 1.56: 3896 1.56 - 1.68: 2 1.68 - 1.81: 46 Bond restraints: 6620 Sorted by residual: bond pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " ideal model delta sigma weight residual 1.798 1.646 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " ideal model delta sigma weight residual 1.798 1.646 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" CD RGP A 801 " pdb=" OE2 RGP A 801 " ideal model delta sigma weight residual 1.302 1.395 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CD RGP B 801 " pdb=" OE2 RGP B 801 " ideal model delta sigma weight residual 1.302 1.395 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" N VAL A 455 " pdb=" CA VAL A 455 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.25e-02 6.40e+03 3.13e+00 ... (remaining 6615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8772 2.32 - 4.64: 150 4.64 - 6.95: 34 6.95 - 9.27: 6 9.27 - 11.59: 2 Bond angle restraints: 8964 Sorted by residual: angle pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " pdb=" OA3 RGP B 801 " ideal model delta sigma weight residual 97.78 109.37 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " pdb=" OA3 RGP A 801 " ideal model delta sigma weight residual 97.78 109.37 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CG RGP B 801 " pdb=" CD RGP B 801 " pdb=" OE2 RGP B 801 " ideal model delta sigma weight residual 112.09 119.96 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CG RGP A 801 " pdb=" CD RGP A 801 " pdb=" OE2 RGP A 801 " ideal model delta sigma weight residual 112.09 119.96 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" N ARG A 544 " pdb=" CA ARG A 544 " pdb=" C ARG A 544 " ideal model delta sigma weight residual 114.75 111.53 3.22 1.26e+00 6.30e-01 6.53e+00 ... (remaining 8959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 3506 16.01 - 32.02: 416 32.02 - 48.02: 98 48.02 - 64.03: 18 64.03 - 80.04: 14 Dihedral angle restraints: 4052 sinusoidal: 1588 harmonic: 2464 Sorted by residual: dihedral pdb=" CA ILE A 732 " pdb=" C ILE A 732 " pdb=" N HIS A 733 " pdb=" CA HIS A 733 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE B 732 " pdb=" C ILE B 732 " pdb=" N HIS B 733 " pdb=" CA HIS B 733 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 366 " pdb=" C THR A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta harmonic sigma weight residual 180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 562 0.030 - 0.059: 276 0.059 - 0.089: 136 0.089 - 0.118: 52 0.118 - 0.148: 22 Chirality restraints: 1048 Sorted by residual: chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE B 574 " pdb=" N ILE B 574 " pdb=" C ILE B 574 " pdb=" CB ILE B 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL B 519 " pdb=" N VAL B 519 " pdb=" C VAL B 519 " pdb=" CB VAL B 519 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1045 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 644 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 643 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 644 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 664 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 665 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.018 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 364 2.70 - 3.25: 7708 3.25 - 3.80: 10395 3.80 - 4.35: 12380 4.35 - 4.90: 20239 Nonbonded interactions: 51086 Sorted by model distance: nonbonded pdb=" O ILE A 429 " pdb=" OG SER A 433 " model vdw 2.148 3.040 nonbonded pdb=" O ILE B 429 " pdb=" OG SER B 433 " model vdw 2.148 3.040 nonbonded pdb=" O ALA A 509 " pdb=" OG1 THR A 512 " model vdw 2.181 3.040 nonbonded pdb=" O ALA B 509 " pdb=" OG1 THR B 512 " model vdw 2.181 3.040 nonbonded pdb=" O CYS B 570 " pdb=" ND1 HIS B 571 " model vdw 2.224 3.120 ... (remaining 51081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.680 Find NCS groups from input model: 0.060 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.008 0.152 6620 Z= 0.363 Angle : 0.875 11.589 8964 Z= 0.460 Chirality : 0.046 0.148 1048 Planarity : 0.005 0.043 1174 Dihedral : 15.473 80.038 2456 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.22 % Favored : 81.78 % Rotamer: Outliers : 0.58 % Allowed : 11.88 % Favored : 87.54 % 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: -4.77 (0.24), residues: 856 helix: -2.25 (0.22), residues: 354 sheet: -4.26 (0.37), residues: 112 loop : -3.68 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 551 TYR 0.011 0.002 TYR A 654 PHE 0.009 0.002 PHE B 387 TRP 0.003 0.001 TRP B 748 HIS 0.007 0.002 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.36 ( 6620) covalent geometry : angle 0.87497 / 0.46 ( 8964) hydrogen bonds : bond 0.18356 / 12.02 ( 300) hydrogen bonds : angle 7.32348 / 5.34 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8727 (t80) cc_final: 0.8397 (t80) REVERT: A 396 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (pp) REVERT: A 487 LEU cc_start: 0.8871 (tp) cc_final: 0.8670 (tp) REVERT: A 505 LEU cc_start: 0.7996 (mt) cc_final: 0.7767 (mt) REVERT: A 534 MET cc_start: 0.8501 (tmm) cc_final: 0.7827 (tmm) REVERT: A 575 ASP cc_start: 0.8038 (t70) cc_final: 0.7835 (t70) REVERT: A 577 ASP cc_start: 0.8501 (t70) cc_final: 0.8147 (t70) REVERT: B 387 PHE cc_start: 0.8717 (t80) cc_final: 0.8386 (t80) REVERT: B 505 LEU cc_start: 0.8076 (mt) cc_final: 0.7842 (mt) REVERT: B 534 MET cc_start: 0.8501 (tmm) cc_final: 0.7814 (tmm) REVERT: B 673 HIS cc_start: 0.8915 (t-90) cc_final: 0.8711 (t-170) outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 0.0882 time to fit residues: 15.6328 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 369 GLN A 400 GLN A 571 HIS A 652 HIS A 770 HIS B 354 ASN B 369 GLN B 400 GLN B 571 HIS B 652 HIS B 770 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095269 restraints weight = 11981.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098613 restraints weight = 8013.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101051 restraints weight = 6025.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102625 restraints weight = 4929.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104008 restraints weight = 4280.926| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6620 Z= 0.190 Angle : 0.710 8.493 8964 Z= 0.372 Chirality : 0.046 0.169 1048 Planarity : 0.006 0.042 1174 Dihedral : 5.675 36.702 934 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.29 % Allowed : 7.25 % Favored : 92.46 % 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: -3.14 (0.27), residues: 856 helix: -0.53 (0.25), residues: 372 sheet: -3.71 (0.35), residues: 140 loop : -3.06 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 585 TYR 0.009 0.001 TYR A 573 PHE 0.018 0.002 PHE A 760 TRP 0.008 0.002 TRP B 768 HIS 0.009 0.001 HIS B 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 6620) covalent geometry : angle 0.71031 / 0.37 ( 8964) hydrogen bonds : bond 0.04459 / 3.00 ( 300) hydrogen bonds : angle 5.12133 / 3.75 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8319 (t0) REVERT: A 487 LEU cc_start: 0.8496 (tp) cc_final: 0.8295 (tp) REVERT: A 505 LEU cc_start: 0.8134 (mt) cc_final: 0.7851 (mt) REVERT: A 534 MET cc_start: 0.8429 (tmm) cc_final: 0.7904 (tmm) REVERT: A 724 GLU cc_start: 0.8612 (pp20) cc_final: 0.8293 (pt0) REVERT: B 354 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8299 (t0) REVERT: B 505 LEU cc_start: 0.8089 (mt) cc_final: 0.7825 (mt) REVERT: B 534 MET cc_start: 0.8416 (tmm) cc_final: 0.7897 (tmm) REVERT: B 724 GLU cc_start: 0.8600 (pp20) cc_final: 0.8263 (pt0) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.0618 time to fit residues: 12.1766 Evaluate side-chains 108 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.128799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100138 restraints weight = 11530.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103731 restraints weight = 7365.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106311 restraints weight = 5431.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108159 restraints weight = 4382.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109485 restraints weight = 3759.488| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6620 Z= 0.142 Angle : 0.656 8.802 8964 Z= 0.336 Chirality : 0.043 0.160 1048 Planarity : 0.005 0.039 1174 Dihedral : 5.311 36.104 934 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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: -2.31 (0.28), residues: 856 helix: 0.15 (0.26), residues: 372 sheet: -3.13 (0.36), residues: 142 loop : -2.69 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 588 TYR 0.006 0.001 TYR A 654 PHE 0.014 0.001 PHE A 616 TRP 0.006 0.001 TRP B 768 HIS 0.004 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6620) covalent geometry : angle 0.65585 / 0.34 ( 8964) hydrogen bonds : bond 0.03905 / 2.63 ( 300) hydrogen bonds : angle 4.74155 / 3.44 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LEU cc_start: 0.6846 (tp) cc_final: 0.6104 (tp) REVERT: B 662 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6908 (mm-30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0620 time to fit residues: 13.4349 Evaluate side-chains 111 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 475 GLN B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101538 restraints weight = 11414.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105208 restraints weight = 7359.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107933 restraints weight = 5409.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109917 restraints weight = 4331.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111097 restraints weight = 3673.075| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6620 Z= 0.128 Angle : 0.678 10.898 8964 Z= 0.334 Chirality : 0.043 0.155 1048 Planarity : 0.005 0.038 1174 Dihedral : 5.071 35.519 934 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.28), residues: 856 helix: 0.51 (0.26), residues: 376 sheet: -2.65 (0.37), residues: 140 loop : -2.53 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 585 TYR 0.008 0.001 TYR A 654 PHE 0.013 0.001 PHE A 760 TRP 0.005 0.001 TRP A 748 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6620) covalent geometry : angle 0.67758 / 0.33 ( 8964) hydrogen bonds : bond 0.03505 / 2.36 ( 300) hydrogen bonds : angle 4.45658 / 3.25 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 LEU cc_start: 0.7806 (mt) cc_final: 0.7298 (mp) REVERT: A 601 MET cc_start: 0.8357 (tmm) cc_final: 0.7406 (tmm) REVERT: B 601 MET cc_start: 0.8352 (tmm) cc_final: 0.7525 (tmm) REVERT: B 662 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6882 (mm-30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0671 time to fit residues: 15.2294 Evaluate side-chains 125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 chunk 24 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 overall best weight: 0.6048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 475 GLN B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102387 restraints weight = 11721.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106211 restraints weight = 7265.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109075 restraints weight = 5219.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111067 restraints weight = 4106.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112602 restraints weight = 3455.465| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6620 Z= 0.132 Angle : 0.682 9.327 8964 Z= 0.337 Chirality : 0.044 0.175 1048 Planarity : 0.004 0.037 1174 Dihedral : 5.070 35.127 934 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -1.73 (0.28), residues: 856 helix: 0.54 (0.26), residues: 376 sheet: -2.86 (0.35), residues: 132 loop : -2.31 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.008 0.001 TYR A 654 PHE 0.023 0.002 PHE B 616 TRP 0.004 0.001 TRP A 768 HIS 0.003 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6620) covalent geometry : angle 0.68248 / 0.34 ( 8964) hydrogen bonds : bond 0.03400 / 2.27 ( 300) hydrogen bonds : angle 4.43346 / 3.24 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LYS cc_start: 0.8432 (tppp) cc_final: 0.8214 (tmtt) REVERT: A 601 MET cc_start: 0.8559 (tmm) cc_final: 0.8147 (tmm) REVERT: A 604 LEU cc_start: 0.9224 (tt) cc_final: 0.9017 (tp) REVERT: A 695 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 601 MET cc_start: 0.8644 (tmm) cc_final: 0.8231 (tmm) REVERT: B 695 GLN cc_start: 0.8875 (tt0) cc_final: 0.8652 (tm-30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0534 time to fit residues: 12.3417 Evaluate side-chains 126 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 64 optimal weight: 0.0270 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102587 restraints weight = 11777.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106480 restraints weight = 7550.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109336 restraints weight = 5539.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111487 restraints weight = 4428.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112934 restraints weight = 3738.127| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6620 Z= 0.126 Angle : 0.671 9.822 8964 Z= 0.334 Chirality : 0.044 0.171 1048 Planarity : 0.004 0.038 1174 Dihedral : 4.968 34.642 934 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -1.47 (0.28), residues: 856 helix: 0.74 (0.26), residues: 378 sheet: -2.57 (0.37), residues: 132 loop : -2.26 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 525 TYR 0.007 0.001 TYR A 654 PHE 0.010 0.001 PHE A 760 TRP 0.008 0.001 TRP A 748 HIS 0.006 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6620) covalent geometry : angle 0.67086 / 0.33 ( 8964) hydrogen bonds : bond 0.03299 / 2.17 ( 300) hydrogen bonds : angle 4.34219 / 3.14 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8493 (tmm) cc_final: 0.8043 (tmm) REVERT: B 505 LEU cc_start: 0.7824 (mt) cc_final: 0.7271 (mp) REVERT: B 570 CYS cc_start: 0.8225 (m) cc_final: 0.8003 (m) REVERT: B 601 MET cc_start: 0.8504 (tmm) cc_final: 0.8071 (tmm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0530 time to fit residues: 12.6542 Evaluate side-chains 120 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103404 restraints weight = 11610.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107198 restraints weight = 7478.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110006 restraints weight = 5480.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112037 restraints weight = 4383.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113370 restraints weight = 3718.833| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6620 Z= 0.133 Angle : 0.677 8.497 8964 Z= 0.337 Chirality : 0.044 0.166 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.891 34.312 934 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -1.24 (0.29), residues: 856 helix: 0.94 (0.27), residues: 378 sheet: -2.41 (0.38), residues: 132 loop : -2.16 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 625 TYR 0.012 0.001 TYR B 654 PHE 0.023 0.002 PHE A 616 TRP 0.008 0.001 TRP A 748 HIS 0.005 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6620) covalent geometry : angle 0.67704 / 0.34 ( 8964) hydrogen bonds : bond 0.03189 / 2.13 ( 300) hydrogen bonds : angle 4.24148 / 3.05 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LEU cc_start: 0.8582 (mp) cc_final: 0.8373 (mp) REVERT: A 601 MET cc_start: 0.8438 (tmm) cc_final: 0.8005 (tmm) REVERT: B 570 CYS cc_start: 0.8250 (m) cc_final: 0.7983 (m) REVERT: B 601 MET cc_start: 0.8448 (tmm) cc_final: 0.8103 (tmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0539 time to fit residues: 12.2489 Evaluate side-chains 122 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 565 HIS B 565 HIS B 673 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102396 restraints weight = 11806.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106238 restraints weight = 7566.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109137 restraints weight = 5569.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111265 restraints weight = 4456.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112782 restraints weight = 3771.079| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6620 Z= 0.140 Angle : 0.693 9.717 8964 Z= 0.346 Chirality : 0.045 0.179 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.886 34.156 934 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -1.21 (0.29), residues: 856 helix: 0.92 (0.26), residues: 378 sheet: -2.36 (0.39), residues: 132 loop : -2.11 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 625 TYR 0.009 0.001 TYR B 654 PHE 0.012 0.001 PHE A 696 TRP 0.006 0.001 TRP B 748 HIS 0.004 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6620) covalent geometry : angle 0.69288 / 0.35 ( 8964) hydrogen bonds : bond 0.03153 / 2.10 ( 300) hydrogen bonds : angle 4.36602 / 3.16 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8349 (tmm) cc_final: 0.8011 (tmm) REVERT: A 662 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 428 GLN cc_start: 0.8778 (mp10) cc_final: 0.8554 (mp10) REVERT: B 601 MET cc_start: 0.8441 (tmm) cc_final: 0.8120 (tmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0482 time to fit residues: 10.7915 Evaluate side-chains 116 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103289 restraints weight = 11885.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107271 restraints weight = 7563.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110152 restraints weight = 5518.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112074 restraints weight = 4405.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113749 restraints weight = 3761.392| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6620 Z= 0.126 Angle : 0.674 9.011 8964 Z= 0.335 Chirality : 0.044 0.173 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.789 34.178 934 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.09 (0.29), residues: 856 helix: 0.97 (0.27), residues: 378 sheet: -2.23 (0.40), residues: 132 loop : -2.01 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 625 TYR 0.009 0.001 TYR B 654 PHE 0.028 0.002 PHE B 616 TRP 0.015 0.002 TRP B 768 HIS 0.004 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6620) covalent geometry : angle 0.67421 / 0.34 ( 8964) hydrogen bonds : bond 0.03093 / 2.06 ( 300) hydrogen bonds : angle 4.24238 / 3.07 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.8321 (tmm) cc_final: 0.7977 (tmm) REVERT: A 662 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6943 (mm-30) REVERT: B 601 MET cc_start: 0.8413 (tmm) cc_final: 0.8044 (tmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0509 time to fit residues: 11.6366 Evaluate side-chains 117 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 70 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105865 restraints weight = 11225.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109681 restraints weight = 7117.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112548 restraints weight = 5173.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114566 restraints weight = 4096.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116137 restraints weight = 3447.994| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6620 Z= 0.123 Angle : 0.687 9.027 8964 Z= 0.341 Chirality : 0.044 0.175 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.768 33.965 934 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.99 (0.29), residues: 856 helix: 0.98 (0.27), residues: 378 sheet: -2.10 (0.40), residues: 132 loop : -1.91 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.008 0.001 TYR A 654 PHE 0.033 0.002 PHE B 696 TRP 0.006 0.001 TRP A 748 HIS 0.004 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6620) covalent geometry : angle 0.68679 / 0.34 ( 8964) hydrogen bonds : bond 0.03047 / 2.04 ( 300) hydrogen bonds : angle 4.17847 / 2.99 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8362 (tmm) cc_final: 0.7999 (tmm) REVERT: A 662 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6919 (mm-30) REVERT: B 353 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8419 (mm-30) REVERT: B 570 CYS cc_start: 0.8224 (m) cc_final: 0.7948 (m) REVERT: B 601 MET cc_start: 0.8393 (tmm) cc_final: 0.8071 (tmm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0506 time to fit residues: 11.1333 Evaluate side-chains 121 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103843 restraints weight = 11814.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107638 restraints weight = 7754.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110214 restraints weight = 5784.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112289 restraints weight = 4719.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113803 restraints weight = 4025.111| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6620 Z= 0.144 Angle : 0.693 8.714 8964 Z= 0.346 Chirality : 0.044 0.170 1048 Planarity : 0.005 0.036 1174 Dihedral : 4.892 33.751 934 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.95 (0.29), residues: 856 helix: 0.95 (0.26), residues: 380 sheet: -2.06 (0.41), residues: 132 loop : -1.82 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.009 0.002 TYR A 573 PHE 0.033 0.003 PHE B 696 TRP 0.012 0.002 TRP B 768 HIS 0.004 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6620) covalent geometry : angle 0.69254 / 0.35 ( 8964) hydrogen bonds : bond 0.03087 / 2.06 ( 300) hydrogen bonds : angle 4.29926 / 3.09 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.47 seconds wall clock time: 19 minutes 44.41 seconds (1184.41 seconds total)