Starting phenix.real_space_refine on Sat May 10 07:30:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvv_37873/05_2025/8wvv_37873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvv_37873/05_2025/8wvv_37873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvv_37873/05_2025/8wvv_37873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvv_37873/05_2025/8wvv_37873.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvv_37873/05_2025/8wvv_37873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvv_37873/05_2025/8wvv_37873.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.044 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 26 5.16 5 C 3643 2.51 5 N 918 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5596 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5596 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 682} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.74, per 1000 atoms: 0.67 Number of scatterers: 5596 At special positions: 0 Unit cell: (77.08, 93.48, 136.94, 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 26 16.00 O 1009 8.00 N 918 7.00 C 3643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=1.99 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 781.1 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 5 sheets defined 33.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.694A pdb=" N ALA A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 466 through 474 removed outlier: 4.158A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.665A pdb=" N ASN A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.837A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.915A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 644 removed outlier: 4.319A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 658 through 675 removed outlier: 3.560A pdb=" N PHE A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.214A pdb=" N LEU A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 729 removed outlier: 3.846A pdb=" N LEU A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 768 removed outlier: 3.564A pdb=" N ASN A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 780 through 789 Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.728A pdb=" N ASN A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 817 removed outlier: 3.715A pdb=" N LEU A 814 " --> pdb=" O GLU A 810 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 5.841A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 62 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 110 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 134 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 206 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 304 removed outlier: 7.578A pdb=" N LEU A 301 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR A 327 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE A 303 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 169 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 891 1.30 - 1.43: 1491 1.43 - 1.56: 3309 1.56 - 1.69: 1 1.69 - 1.82: 35 Bond restraints: 5727 Sorted by residual: bond pdb=" C ASN A 805 " pdb=" N PRO A 806 " ideal model delta sigma weight residual 1.335 1.507 -0.172 1.19e-02 7.06e+03 2.09e+02 bond pdb=" C TYR A 468 " pdb=" O TYR A 468 " ideal model delta sigma weight residual 1.236 1.341 -0.105 1.26e-02 6.30e+03 6.88e+01 bond pdb=" C PHE A 759 " pdb=" O PHE A 759 " ideal model delta sigma weight residual 1.236 1.308 -0.072 1.15e-02 7.56e+03 3.89e+01 bond pdb=" CA SER A 690 " pdb=" CB SER A 690 " ideal model delta sigma weight residual 1.538 1.459 0.079 1.38e-02 5.25e+03 3.32e+01 bond pdb=" C ILE A 758 " pdb=" O ILE A 758 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.12e-02 7.97e+03 3.31e+01 ... (remaining 5722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 7691 4.83 - 9.67: 81 9.67 - 14.50: 12 14.50 - 19.33: 3 19.33 - 24.17: 1 Bond angle restraints: 7788 Sorted by residual: angle pdb=" N ALA A 689 " pdb=" CA ALA A 689 " pdb=" C ALA A 689 " ideal model delta sigma weight residual 114.62 90.45 24.17 1.14e+00 7.69e-01 4.49e+02 angle pdb=" C ASN A 805 " pdb=" N PRO A 806 " pdb=" CA PRO A 806 " ideal model delta sigma weight residual 119.56 135.00 -15.44 1.02e+00 9.61e-01 2.29e+02 angle pdb=" C TYR A 801 " pdb=" CA TYR A 801 " pdb=" CB TYR A 801 " ideal model delta sigma weight residual 110.79 92.20 18.59 1.66e+00 3.63e-01 1.25e+02 angle pdb=" N SER A 573 " pdb=" CA SER A 573 " pdb=" C SER A 573 " ideal model delta sigma weight residual 113.18 101.03 12.15 1.21e+00 6.83e-01 1.01e+02 angle pdb=" C LEU A 575 " pdb=" N PHE A 576 " pdb=" CA PHE A 576 " ideal model delta sigma weight residual 120.54 108.55 11.99 1.35e+00 5.49e-01 7.88e+01 ... (remaining 7783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2845 16.90 - 33.80: 422 33.80 - 50.70: 106 50.70 - 67.59: 20 67.59 - 84.49: 9 Dihedral angle restraints: 3402 sinusoidal: 1318 harmonic: 2084 Sorted by residual: dihedral pdb=" C TYR A 801 " pdb=" N TYR A 801 " pdb=" CA TYR A 801 " pdb=" CB TYR A 801 " ideal model delta harmonic sigma weight residual -122.60 -98.42 -24.18 0 2.50e+00 1.60e-01 9.36e+01 dihedral pdb=" C PHE A 804 " pdb=" N PHE A 804 " pdb=" CA PHE A 804 " pdb=" CB PHE A 804 " ideal model delta harmonic sigma weight residual -122.60 -145.59 22.99 0 2.50e+00 1.60e-01 8.46e+01 dihedral pdb=" C SER A 688 " pdb=" N SER A 688 " pdb=" CA SER A 688 " pdb=" CB SER A 688 " ideal model delta harmonic sigma weight residual -122.60 -101.73 -20.87 0 2.50e+00 1.60e-01 6.97e+01 ... (remaining 3399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 901 0.178 - 0.357: 10 0.357 - 0.535: 7 0.535 - 0.713: 1 0.713 - 0.892: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA PHE A 804 " pdb=" N PHE A 804 " pdb=" C PHE A 804 " pdb=" CB PHE A 804 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PHE A 803 " pdb=" N PHE A 803 " pdb=" C PHE A 803 " pdb=" CB PHE A 803 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CA SER A 688 " pdb=" N SER A 688 " pdb=" C SER A 688 " pdb=" CB SER A 688 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 917 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 562 " -0.033 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C THR A 562 " 0.116 2.00e-02 2.50e+03 pdb=" O THR A 562 " -0.044 2.00e-02 2.50e+03 pdb=" N THR A 563 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 679 " -0.099 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO A 680 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 680 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 680 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 570 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO A 571 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.063 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 15 2.33 - 2.98: 3001 2.98 - 3.62: 8782 3.62 - 4.26: 13457 4.26 - 4.90: 21703 Nonbonded interactions: 46958 Sorted by model distance: nonbonded pdb=" O GLY A 592 " pdb=" CD2 PHE A 596 " model vdw 1.693 3.340 nonbonded pdb=" CD2 PHE A 555 " pdb=" CG2 VAL A 799 " model vdw 1.729 3.760 nonbonded pdb=" CE2 PHE A 555 " pdb=" CG2 VAL A 799 " model vdw 2.171 3.760 nonbonded pdb=" O VAL A 153 " pdb=" OG1 THR A 178 " model vdw 2.174 3.040 nonbonded pdb=" O VAL A 711 " pdb=" OG SER A 715 " model vdw 2.179 3.040 ... (remaining 46953 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.007 0.172 5732 Z= 0.482 Angle : 1.273 24.165 7798 Z= 0.819 Chirality : 0.077 0.892 920 Planarity : 0.010 0.142 981 Dihedral : 17.092 84.492 2025 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.28 % Allowed : 25.68 % Favored : 73.05 % Cbeta Deviations : 1.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.30), residues: 704 helix: -1.61 (0.32), residues: 228 sheet: -3.17 (0.60), residues: 72 loop : -1.71 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 812 HIS 0.003 0.001 HIS A 171 PHE 0.045 0.002 PHE A 808 TYR 0.028 0.002 TYR A 801 ARG 0.003 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.27958 ( 169) hydrogen bonds : angle 9.96559 ( 498) SS BOND : bond 0.02651 ( 5) SS BOND : angle 5.91326 ( 10) covalent geometry : bond 0.00692 ( 5727) covalent geometry : angle 1.25654 ( 7788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 HIS cc_start: 0.7810 (t70) cc_final: 0.7363 (t70) REVERT: A 371 SER cc_start: 0.8914 (p) cc_final: 0.8545 (p) REVERT: A 762 PRO cc_start: 0.8048 (Cg_exo) cc_final: 0.7806 (Cg_endo) outliers start: 8 outliers final: 7 residues processed: 117 average time/residue: 0.1463 time to fit residues: 23.3707 Evaluate side-chains 109 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 571 PRO Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 783 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS A 171 HIS ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS A 417 ASN A 458 ASN A 584 ASN A 748 HIS A 797 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.126753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104368 restraints weight = 12119.677| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.75 r_work: 0.3567 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5732 Z= 0.167 Angle : 0.680 8.175 7798 Z= 0.343 Chirality : 0.045 0.171 920 Planarity : 0.006 0.076 981 Dihedral : 5.952 57.827 757 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.31 % Allowed : 24.24 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.30), residues: 704 helix: -0.93 (0.32), residues: 224 sheet: -3.13 (0.57), residues: 72 loop : -1.66 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.005 0.001 HIS A 748 PHE 0.036 0.002 PHE A 596 TYR 0.021 0.002 TYR A 280 ARG 0.003 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 169) hydrogen bonds : angle 5.84780 ( 498) SS BOND : bond 0.00667 ( 5) SS BOND : angle 1.74621 ( 10) covalent geometry : bond 0.00370 ( 5727) covalent geometry : angle 0.67712 ( 7788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8022 (t80) cc_final: 0.7471 (t80) REVERT: A 204 VAL cc_start: 0.8234 (m) cc_final: 0.8016 (m) REVERT: A 231 ASP cc_start: 0.7199 (t0) cc_final: 0.6952 (t0) REVERT: A 245 LYS cc_start: 0.8803 (tttt) cc_final: 0.8336 (tppt) REVERT: A 252 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: A 273 LEU cc_start: 0.8854 (mm) cc_final: 0.8148 (tp) REVERT: A 279 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 371 SER cc_start: 0.9124 (p) cc_final: 0.8769 (p) REVERT: A 442 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 520 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7728 (mp) REVERT: A 728 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7624 (mm) REVERT: A 731 ASN cc_start: 0.8048 (p0) cc_final: 0.7540 (t0) REVERT: A 754 PHE cc_start: 0.8223 (t80) cc_final: 0.8016 (t80) REVERT: A 759 PHE cc_start: 0.7677 (m-10) cc_final: 0.7436 (m-10) REVERT: A 783 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7259 (tptp) REVERT: A 808 PHE cc_start: 0.8238 (t80) cc_final: 0.7940 (t80) REVERT: A 814 LEU cc_start: 0.8128 (tt) cc_final: 0.7863 (mt) outliers start: 27 outliers final: 12 residues processed: 134 average time/residue: 0.1196 time to fit residues: 23.2495 Evaluate side-chains 125 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.125993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103532 restraints weight = 12285.183| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.72 r_work: 0.3544 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5732 Z= 0.135 Angle : 0.630 9.106 7798 Z= 0.311 Chirality : 0.044 0.174 920 Planarity : 0.005 0.064 981 Dihedral : 5.159 50.313 749 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.47 % Allowed : 23.76 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.30), residues: 704 helix: -0.45 (0.32), residues: 226 sheet: -3.21 (0.56), residues: 72 loop : -1.61 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 751 HIS 0.003 0.001 HIS A 97 PHE 0.018 0.001 PHE A 808 TYR 0.016 0.002 TYR A 280 ARG 0.002 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 169) hydrogen bonds : angle 5.30138 ( 498) SS BOND : bond 0.00471 ( 5) SS BOND : angle 1.65183 ( 10) covalent geometry : bond 0.00311 ( 5727) covalent geometry : angle 0.62792 ( 7788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.7574 (t0) cc_final: 0.7295 (t0) REVERT: A 245 LYS cc_start: 0.8815 (tttt) cc_final: 0.8359 (tppt) REVERT: A 252 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: A 273 LEU cc_start: 0.8878 (mm) cc_final: 0.8164 (tp) REVERT: A 279 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8295 (pp) REVERT: A 371 SER cc_start: 0.9163 (p) cc_final: 0.8809 (p) REVERT: A 395 ASP cc_start: 0.7828 (t70) cc_final: 0.7370 (t0) REVERT: A 520 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 728 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7638 (mm) REVERT: A 731 ASN cc_start: 0.7984 (p0) cc_final: 0.7398 (t0) REVERT: A 783 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7335 (tptp) REVERT: A 814 LEU cc_start: 0.8259 (tt) cc_final: 0.8052 (mt) outliers start: 28 outliers final: 12 residues processed: 131 average time/residue: 0.1202 time to fit residues: 22.6752 Evaluate side-chains 120 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102053 restraints weight = 12663.259| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.70 r_work: 0.3525 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5732 Z= 0.159 Angle : 0.645 8.300 7798 Z= 0.319 Chirality : 0.045 0.166 920 Planarity : 0.005 0.066 981 Dihedral : 5.052 45.982 746 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.42 % Allowed : 25.36 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.30), residues: 704 helix: -0.39 (0.33), residues: 233 sheet: -3.16 (0.56), residues: 72 loop : -1.60 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.017 0.001 PHE A 808 TYR 0.020 0.002 TYR A 801 ARG 0.002 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 169) hydrogen bonds : angle 5.16392 ( 498) SS BOND : bond 0.00490 ( 5) SS BOND : angle 1.78047 ( 10) covalent geometry : bond 0.00370 ( 5727) covalent geometry : angle 0.64258 ( 7788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.644 Fit side-chains REVERT: A 231 ASP cc_start: 0.7604 (t0) cc_final: 0.7322 (t0) REVERT: A 245 LYS cc_start: 0.8774 (tttt) cc_final: 0.8518 (mmtm) REVERT: A 252 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: A 273 LEU cc_start: 0.8925 (mm) cc_final: 0.8258 (tp) REVERT: A 279 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8458 (pp) REVERT: A 371 SER cc_start: 0.9142 (p) cc_final: 0.8791 (p) REVERT: A 395 ASP cc_start: 0.7803 (t70) cc_final: 0.7414 (t0) REVERT: A 416 THR cc_start: 0.8838 (m) cc_final: 0.8550 (t) REVERT: A 442 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8439 (t) REVERT: A 473 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 728 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7615 (mm) REVERT: A 783 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7576 (tptp) REVERT: A 814 LEU cc_start: 0.8311 (tt) cc_final: 0.7977 (mt) outliers start: 34 outliers final: 16 residues processed: 132 average time/residue: 0.1253 time to fit residues: 23.7220 Evaluate side-chains 129 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103030 restraints weight = 12452.666| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.70 r_work: 0.3544 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5732 Z= 0.130 Angle : 0.602 8.091 7798 Z= 0.298 Chirality : 0.044 0.148 920 Planarity : 0.004 0.065 981 Dihedral : 4.831 43.269 746 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.47 % Allowed : 24.88 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.31), residues: 704 helix: -0.17 (0.33), residues: 232 sheet: -3.12 (0.57), residues: 72 loop : -1.54 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.002 0.001 HIS A 97 PHE 0.017 0.001 PHE A 808 TYR 0.015 0.002 TYR A 801 ARG 0.002 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 169) hydrogen bonds : angle 4.98444 ( 498) SS BOND : bond 0.00442 ( 5) SS BOND : angle 1.53754 ( 10) covalent geometry : bond 0.00305 ( 5727) covalent geometry : angle 0.59994 ( 7788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.595 Fit side-chains REVERT: A 231 ASP cc_start: 0.7644 (t0) cc_final: 0.7376 (t0) REVERT: A 245 LYS cc_start: 0.8714 (tttt) cc_final: 0.8424 (mmtm) REVERT: A 252 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: A 273 LEU cc_start: 0.8905 (mm) cc_final: 0.8242 (tp) REVERT: A 279 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 371 SER cc_start: 0.9109 (p) cc_final: 0.8754 (p) REVERT: A 395 ASP cc_start: 0.7763 (t70) cc_final: 0.7335 (t0) REVERT: A 416 THR cc_start: 0.8798 (m) cc_final: 0.8494 (t) REVERT: A 473 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7101 (t80) REVERT: A 728 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 814 LEU cc_start: 0.8231 (tt) cc_final: 0.7819 (mt) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 0.1247 time to fit residues: 22.5874 Evaluate side-chains 126 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.123836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101382 restraints weight = 12328.097| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.70 r_work: 0.3519 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5732 Z= 0.153 Angle : 0.618 7.792 7798 Z= 0.306 Chirality : 0.045 0.150 920 Planarity : 0.004 0.065 981 Dihedral : 4.427 31.631 742 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.31 % Allowed : 25.04 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.31), residues: 704 helix: -0.21 (0.33), residues: 232 sheet: -3.15 (0.57), residues: 72 loop : -1.57 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.003 0.001 HIS A 157 PHE 0.017 0.001 PHE A 808 TYR 0.016 0.002 TYR A 801 ARG 0.002 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 169) hydrogen bonds : angle 5.02298 ( 498) SS BOND : bond 0.00491 ( 5) SS BOND : angle 1.56662 ( 10) covalent geometry : bond 0.00361 ( 5727) covalent geometry : angle 0.61566 ( 7788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.648 Fit side-chains REVERT: A 231 ASP cc_start: 0.7643 (t0) cc_final: 0.7347 (t0) REVERT: A 245 LYS cc_start: 0.8657 (tttt) cc_final: 0.8358 (mmtm) REVERT: A 252 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: A 273 LEU cc_start: 0.8915 (mm) cc_final: 0.8255 (tp) REVERT: A 279 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 371 SER cc_start: 0.9128 (p) cc_final: 0.8758 (p) REVERT: A 395 ASP cc_start: 0.7771 (t70) cc_final: 0.7363 (t0) REVERT: A 416 THR cc_start: 0.8782 (m) cc_final: 0.8487 (t) REVERT: A 473 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7091 (t80) REVERT: A 728 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 731 ASN cc_start: 0.7647 (p0) cc_final: 0.7328 (p0) REVERT: A 783 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7544 (tptp) REVERT: A 814 LEU cc_start: 0.8266 (tt) cc_final: 0.8041 (tt) outliers start: 27 outliers final: 17 residues processed: 118 average time/residue: 0.1176 time to fit residues: 19.9609 Evaluate side-chains 121 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.125737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103510 restraints weight = 12310.426| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.69 r_work: 0.3554 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5732 Z= 0.120 Angle : 0.589 7.807 7798 Z= 0.292 Chirality : 0.043 0.142 920 Planarity : 0.004 0.064 981 Dihedral : 4.242 29.466 742 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.15 % Allowed : 26.16 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.31), residues: 704 helix: -0.01 (0.34), residues: 232 sheet: -2.91 (0.64), residues: 62 loop : -1.54 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE A 808 TYR 0.014 0.001 TYR A 801 ARG 0.002 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 169) hydrogen bonds : angle 4.88146 ( 498) SS BOND : bond 0.00398 ( 5) SS BOND : angle 1.31554 ( 10) covalent geometry : bond 0.00280 ( 5727) covalent geometry : angle 0.58799 ( 7788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.7833 (t80) cc_final: 0.7532 (t80) REVERT: A 182 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 231 ASP cc_start: 0.7630 (t0) cc_final: 0.7295 (t0) REVERT: A 245 LYS cc_start: 0.8569 (tttt) cc_final: 0.8283 (mmtm) REVERT: A 252 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 273 LEU cc_start: 0.8904 (mm) cc_final: 0.8286 (tp) REVERT: A 279 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8439 (pp) REVERT: A 371 SER cc_start: 0.9014 (p) cc_final: 0.8642 (p) REVERT: A 395 ASP cc_start: 0.7768 (t70) cc_final: 0.7346 (t0) REVERT: A 416 THR cc_start: 0.8734 (m) cc_final: 0.8422 (t) REVERT: A 473 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 728 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7549 (mm) REVERT: A 745 MET cc_start: 0.7651 (mmp) cc_final: 0.7425 (tpp) outliers start: 26 outliers final: 15 residues processed: 123 average time/residue: 0.1170 time to fit residues: 20.7210 Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.119114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096436 restraints weight = 12404.834| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.71 r_work: 0.3422 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5732 Z= 0.245 Angle : 0.729 10.459 7798 Z= 0.361 Chirality : 0.048 0.154 920 Planarity : 0.005 0.060 981 Dihedral : 4.863 33.442 742 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.47 % Allowed : 26.00 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.31), residues: 704 helix: -0.39 (0.33), residues: 233 sheet: -3.13 (0.56), residues: 72 loop : -1.62 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 546 HIS 0.004 0.001 HIS A 209 PHE 0.023 0.002 PHE A 706 TYR 0.016 0.002 TYR A 801 ARG 0.003 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 169) hydrogen bonds : angle 5.35676 ( 498) SS BOND : bond 0.00700 ( 5) SS BOND : angle 1.91102 ( 10) covalent geometry : bond 0.00578 ( 5727) covalent geometry : angle 0.72604 ( 7788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.679 Fit side-chains REVERT: A 182 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 231 ASP cc_start: 0.7576 (t0) cc_final: 0.7354 (t0) REVERT: A 245 LYS cc_start: 0.8730 (tttt) cc_final: 0.8415 (mmtm) REVERT: A 252 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: A 273 LEU cc_start: 0.8987 (mm) cc_final: 0.8300 (tp) REVERT: A 371 SER cc_start: 0.9094 (p) cc_final: 0.8719 (p) REVERT: A 395 ASP cc_start: 0.7934 (t70) cc_final: 0.7485 (t0) REVERT: A 473 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 728 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 731 ASN cc_start: 0.7760 (p0) cc_final: 0.7287 (p0) REVERT: A 745 MET cc_start: 0.7806 (mmp) cc_final: 0.7552 (tpp) REVERT: A 783 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7669 (tptp) outliers start: 28 outliers final: 20 residues processed: 122 average time/residue: 0.1367 time to fit residues: 23.5004 Evaluate side-chains 121 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101199 restraints weight = 12433.622| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.68 r_work: 0.3509 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5732 Z= 0.139 Angle : 0.660 10.025 7798 Z= 0.322 Chirality : 0.044 0.146 920 Planarity : 0.004 0.066 981 Dihedral : 4.541 31.934 742 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.15 % Allowed : 26.79 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.31), residues: 704 helix: -0.30 (0.34), residues: 232 sheet: -2.85 (0.64), residues: 59 loop : -1.63 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 474 HIS 0.003 0.001 HIS A 256 PHE 0.018 0.001 PHE A 706 TYR 0.017 0.002 TYR A 234 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 169) hydrogen bonds : angle 5.07120 ( 498) SS BOND : bond 0.00397 ( 5) SS BOND : angle 1.28844 ( 10) covalent geometry : bond 0.00331 ( 5727) covalent geometry : angle 0.65905 ( 7788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8207 (t80) cc_final: 0.7741 (t80) REVERT: A 182 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 245 LYS cc_start: 0.8594 (tttt) cc_final: 0.8248 (mmtm) REVERT: A 252 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 273 LEU cc_start: 0.8952 (mm) cc_final: 0.8318 (tp) REVERT: A 371 SER cc_start: 0.9037 (p) cc_final: 0.8656 (p) REVERT: A 395 ASP cc_start: 0.7816 (t70) cc_final: 0.7399 (t0) REVERT: A 416 THR cc_start: 0.8761 (m) cc_final: 0.8514 (t) REVERT: A 473 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 728 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 745 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7398 (tpp) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.1290 time to fit residues: 21.7967 Evaluate side-chains 122 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.122541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100231 restraints weight = 12368.014| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.68 r_work: 0.3501 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5732 Z= 0.147 Angle : 0.685 13.087 7798 Z= 0.329 Chirality : 0.045 0.148 920 Planarity : 0.005 0.068 981 Dihedral : 4.487 30.649 742 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.99 % Allowed : 27.91 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.31), residues: 704 helix: -0.23 (0.34), residues: 232 sheet: -2.63 (0.71), residues: 47 loop : -1.68 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.001 PHE A 706 TYR 0.015 0.002 TYR A 801 ARG 0.002 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 169) hydrogen bonds : angle 5.06032 ( 498) SS BOND : bond 0.00501 ( 5) SS BOND : angle 1.48943 ( 10) covalent geometry : bond 0.00348 ( 5727) covalent geometry : angle 0.68345 ( 7788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 245 LYS cc_start: 0.8598 (tttt) cc_final: 0.8267 (mmtm) REVERT: A 252 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: A 273 LEU cc_start: 0.8939 (mm) cc_final: 0.8299 (tp) REVERT: A 371 SER cc_start: 0.9009 (p) cc_final: 0.8627 (p) REVERT: A 395 ASP cc_start: 0.7820 (t70) cc_final: 0.7401 (t0) REVERT: A 473 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7215 (t80) REVERT: A 728 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 745 MET cc_start: 0.7727 (mmp) cc_final: 0.7450 (tpp) REVERT: A 783 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7605 (tptp) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.1322 time to fit residues: 21.3966 Evaluate side-chains 121 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103230 restraints weight = 12467.505| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.57 r_work: 0.3565 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5732 Z= 0.125 Angle : 0.660 12.552 7798 Z= 0.317 Chirality : 0.044 0.144 920 Planarity : 0.005 0.069 981 Dihedral : 4.379 29.790 742 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.35 % Allowed : 28.87 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.31), residues: 704 helix: -0.12 (0.34), residues: 232 sheet: -2.63 (0.72), residues: 47 loop : -1.64 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.012 0.001 PHE A 808 TYR 0.016 0.002 TYR A 234 ARG 0.005 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 169) hydrogen bonds : angle 4.93428 ( 498) SS BOND : bond 0.00384 ( 5) SS BOND : angle 1.32005 ( 10) covalent geometry : bond 0.00293 ( 5727) covalent geometry : angle 0.65885 ( 7788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.40 seconds wall clock time: 54 minutes 47.67 seconds (3287.67 seconds total)