Starting phenix.real_space_refine on Fri Aug 22 16:04:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvv_37873/08_2025/8wvv_37873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvv_37873/08_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_37873/08_2025/8wvv_37873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvv_37873/08_2025/8wvv_37873.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvv_37873/08_2025/8wvv_37873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvv_37873/08_2025/8wvv_37873.cif" } resolution = 3.35 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= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.21, per 1000 atoms: 0.22 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: 0.38 Conformation dependent library (CDL) restraints added in 125.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.13 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: 0.67 Time building geometry restraints manager: 0.48 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.320 Find NCS groups from input model: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.700 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 643 TYR 0.028 0.002 TYR A 801 PHE 0.045 0.002 PHE A 808 TRP 0.022 0.002 TRP A 812 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 5727) covalent geometry : angle 1.25654 ( 7788) SS BOND : bond 0.02651 ( 5) SS BOND : angle 5.91326 ( 10) hydrogen bonds : bond 0.27958 ( 169) hydrogen bonds : angle 9.96559 ( 498) *********************** 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 : 0.128 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: 0.7808 (Cg_endo) outliers start: 8 outliers final: 7 residues processed: 117 average time/residue: 0.0491 time to fit residues: 8.0282 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 : 0.150 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.128543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.106096 restraints weight = 12508.429| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.83 r_work: 0.3594 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5732 Z= 0.142 Angle : 0.661 8.305 7798 Z= 0.333 Chirality : 0.044 0.162 920 Planarity : 0.006 0.075 981 Dihedral : 5.900 57.150 757 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.31 % Allowed : 24.08 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -2.37 (0.30), residues: 704 helix: -0.97 (0.32), residues: 224 sheet: -3.11 (0.57), residues: 72 loop : -1.62 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.021 0.002 TYR A 280 PHE 0.037 0.001 PHE A 596 TRP 0.009 0.001 TRP A 474 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5727) covalent geometry : angle 0.65900 ( 7788) SS BOND : bond 0.00550 ( 5) SS BOND : angle 1.57511 ( 10) hydrogen bonds : bond 0.04435 ( 169) hydrogen bonds : angle 5.79718 ( 498) *********************** 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 142 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.7949 (t80) cc_final: 0.7267 (t80) REVERT: A 204 VAL cc_start: 0.8198 (m) cc_final: 0.7967 (m) REVERT: A 231 ASP cc_start: 0.7192 (t0) cc_final: 0.6945 (t0) REVERT: A 245 LYS cc_start: 0.8703 (tttt) cc_final: 0.8264 (tppt) REVERT: A 252 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 273 LEU cc_start: 0.8797 (mm) cc_final: 0.8131 (tp) REVERT: A 279 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8205 (pp) REVERT: A 371 SER cc_start: 0.9098 (p) cc_final: 0.8725 (p) REVERT: A 520 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 728 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7629 (mm) REVERT: A 731 ASN cc_start: 0.7964 (p0) cc_final: 0.7465 (t0) REVERT: A 754 PHE cc_start: 0.8148 (t80) cc_final: 0.7904 (t80) REVERT: A 783 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7272 (tptp) REVERT: A 808 PHE cc_start: 0.8076 (t80) cc_final: 0.7823 (t80) REVERT: A 814 LEU cc_start: 0.8103 (tt) cc_final: 0.7840 (mt) outliers start: 27 outliers final: 12 residues processed: 136 average time/residue: 0.0341 time to fit residues: 6.8178 Evaluate side-chains 124 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 368 GLU 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 58 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 15 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 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 = 0.4030 r_free = 0.4030 target = 0.126925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104596 restraints weight = 12272.764| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.73 r_work: 0.3567 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5732 Z= 0.135 Angle : 0.631 9.183 7798 Z= 0.312 Chirality : 0.043 0.160 920 Planarity : 0.005 0.061 981 Dihedral : 5.100 50.610 750 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.47 % Allowed : 23.60 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -2.04 (0.30), residues: 704 helix: -0.44 (0.32), residues: 224 sheet: -3.08 (0.58), residues: 72 loop : -1.56 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.015 0.002 TYR A 280 PHE 0.017 0.001 PHE A 808 TRP 0.011 0.001 TRP A 751 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5727) covalent geometry : angle 0.62856 ( 7788) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.70684 ( 10) hydrogen bonds : bond 0.04007 ( 169) hydrogen bonds : angle 5.33549 ( 498) *********************** 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 142 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8034 (t80) cc_final: 0.7745 (t80) REVERT: A 165 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6913 (mm) REVERT: A 231 ASP cc_start: 0.7508 (t0) cc_final: 0.7231 (t0) REVERT: A 245 LYS cc_start: 0.8769 (tttt) cc_final: 0.8310 (tppt) REVERT: A 252 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 273 LEU cc_start: 0.8847 (mm) cc_final: 0.8128 (tp) REVERT: A 279 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8265 (pp) REVERT: A 371 SER cc_start: 0.9151 (p) cc_final: 0.8791 (p) REVERT: A 395 ASP cc_start: 0.7809 (t70) cc_final: 0.7378 (t0) REVERT: A 416 THR cc_start: 0.8714 (m) cc_final: 0.8347 (t) REVERT: A 442 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8335 (t) REVERT: A 520 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 642 GLU cc_start: 0.7249 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 728 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7669 (mm) REVERT: A 731 ASN cc_start: 0.7995 (p0) cc_final: 0.7469 (t0) REVERT: A 783 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7394 (tptp) outliers start: 28 outliers final: 13 residues processed: 134 average time/residue: 0.0350 time to fit residues: 6.9783 Evaluate side-chains 122 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 165 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 368 GLU Chi-restraints excluded: chain A residue 389 ILE 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 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 Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 379 GLN ** A 417 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 = 0.4010 r_free = 0.4010 target = 0.125219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102732 restraints weight = 12454.935| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.81 r_work: 0.3531 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5732 Z= 0.141 Angle : 0.626 8.187 7798 Z= 0.310 Chirality : 0.044 0.165 920 Planarity : 0.005 0.063 981 Dihedral : 4.902 45.673 746 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.31 % Allowed : 24.72 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -2.01 (0.30), residues: 704 helix: -0.39 (0.32), residues: 232 sheet: -3.10 (0.57), residues: 72 loop : -1.56 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.018 0.002 TYR A 801 PHE 0.016 0.001 PHE A 808 TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5727) covalent geometry : angle 0.62357 ( 7788) SS BOND : bond 0.00427 ( 5) SS BOND : angle 1.63246 ( 10) hydrogen bonds : bond 0.03764 ( 169) hydrogen bonds : angle 5.14707 ( 498) *********************** 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 138 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.193 Fit side-chains REVERT: A 113 GLN cc_start: 0.7653 (mp10) cc_final: 0.7417 (mp10) REVERT: A 210 ASN cc_start: 0.7446 (m-40) cc_final: 0.7241 (m-40) REVERT: A 231 ASP cc_start: 0.7584 (t0) cc_final: 0.7280 (t0) REVERT: A 245 LYS cc_start: 0.8754 (tttt) cc_final: 0.8311 (tppt) REVERT: A 252 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: A 273 LEU cc_start: 0.8882 (mm) cc_final: 0.8173 (tp) REVERT: A 279 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8358 (pp) REVERT: A 371 SER cc_start: 0.9153 (p) cc_final: 0.8803 (p) REVERT: A 395 ASP cc_start: 0.7864 (t70) cc_final: 0.7442 (t0) REVERT: A 442 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8316 (t) REVERT: A 473 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7042 (t80) REVERT: A 728 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7668 (mm) REVERT: A 783 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7536 (tptp) outliers start: 27 outliers final: 13 residues processed: 127 average time/residue: 0.0439 time to fit residues: 8.1728 Evaluate side-chains 121 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 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 442 VAL 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 595 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.0060 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.0040 chunk 54 optimal weight: 0.4980 chunk 2 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 overall best weight: 0.2608 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104863 restraints weight = 12648.376| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.87 r_work: 0.3568 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5732 Z= 0.109 Angle : 0.604 9.901 7798 Z= 0.295 Chirality : 0.043 0.142 920 Planarity : 0.004 0.060 981 Dihedral : 4.597 41.093 746 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.03 % Allowed : 26.48 % Favored : 70.49 % 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 aren not related in a simple way. whole: -1.85 (0.30), residues: 704 helix: -0.18 (0.33), residues: 232 sheet: -2.99 (0.59), residues: 72 loop : -1.53 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 643 TYR 0.013 0.002 TYR A 801 PHE 0.016 0.001 PHE A 808 TRP 0.010 0.001 TRP A 474 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5727) covalent geometry : angle 0.60264 ( 7788) SS BOND : bond 0.00318 ( 5) SS BOND : angle 1.31113 ( 10) hydrogen bonds : bond 0.03488 ( 169) hydrogen bonds : angle 4.95166 ( 498) *********************** 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 127 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.146 Fit side-chains REVERT: A 231 ASP cc_start: 0.7642 (t0) cc_final: 0.7342 (t0) REVERT: A 245 LYS cc_start: 0.8697 (tttt) cc_final: 0.8386 (mmtm) REVERT: A 252 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: A 273 LEU cc_start: 0.8836 (mm) cc_final: 0.8139 (tp) REVERT: A 279 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (pp) REVERT: A 371 SER cc_start: 0.9105 (p) cc_final: 0.8742 (p) REVERT: A 473 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 728 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7642 (mm) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.0366 time to fit residues: 6.5879 Evaluate side-chains 117 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 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 389 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 745 MET 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 60 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.123889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101063 restraints weight = 12455.277| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.83 r_work: 0.3502 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5732 Z= 0.153 Angle : 0.629 9.876 7798 Z= 0.312 Chirality : 0.044 0.151 920 Planarity : 0.004 0.061 981 Dihedral : 4.366 32.465 742 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.99 % Allowed : 25.04 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -1.93 (0.30), residues: 704 helix: -0.28 (0.33), residues: 230 sheet: -2.96 (0.59), residues: 71 loop : -1.56 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 604 TYR 0.016 0.002 TYR A 801 PHE 0.015 0.001 PHE A 808 TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5727) covalent geometry : angle 0.62662 ( 7788) SS BOND : bond 0.00472 ( 5) SS BOND : angle 1.58811 ( 10) hydrogen bonds : bond 0.03667 ( 169) hydrogen bonds : angle 5.05086 ( 498) *********************** 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 131 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.143 Fit side-chains REVERT: A 95 PHE cc_start: 0.8026 (t80) cc_final: 0.7535 (t80) REVERT: A 231 ASP cc_start: 0.7655 (t0) cc_final: 0.7317 (t0) REVERT: A 245 LYS cc_start: 0.8720 (tttt) cc_final: 0.8353 (mmtm) REVERT: A 252 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: A 273 LEU cc_start: 0.8917 (mm) cc_final: 0.8215 (tp) REVERT: A 279 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8370 (pp) REVERT: A 371 SER cc_start: 0.9160 (p) cc_final: 0.8770 (p) REVERT: A 395 ASP cc_start: 0.7989 (t0) cc_final: 0.7473 (t0) REVERT: A 473 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7129 (t80) REVERT: A 725 TYR cc_start: 0.7575 (t80) cc_final: 0.7337 (t80) REVERT: A 728 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7678 (mm) outliers start: 25 outliers final: 14 residues processed: 121 average time/residue: 0.0438 time to fit residues: 7.8306 Evaluate side-chains 117 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 389 ILE 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 681 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 61 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.125127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102330 restraints weight = 12602.858| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.88 r_work: 0.3520 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3997 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= 0.128 Angle : 0.614 9.989 7798 Z= 0.303 Chirality : 0.044 0.143 920 Planarity : 0.004 0.060 981 Dihedral : 4.238 30.300 742 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.67 % Allowed : 25.20 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -1.71 (0.31), residues: 704 helix: -0.05 (0.34), residues: 231 sheet: -2.88 (0.65), residues: 62 loop : -1.51 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.015 0.002 TYR A 234 PHE 0.015 0.001 PHE A 808 TRP 0.011 0.001 TRP A 539 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5727) covalent geometry : angle 0.61297 ( 7788) SS BOND : bond 0.00382 ( 5) SS BOND : angle 1.34692 ( 10) hydrogen bonds : bond 0.03512 ( 169) hydrogen bonds : angle 4.93890 ( 498) *********************** 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 123 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.207 Fit side-chains REVERT: A 95 PHE cc_start: 0.7999 (t80) cc_final: 0.7561 (t80) REVERT: A 182 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8145 (tp) REVERT: A 231 ASP cc_start: 0.7649 (t0) cc_final: 0.7313 (t0) REVERT: A 245 LYS cc_start: 0.8616 (tttt) cc_final: 0.8264 (mmtm) REVERT: A 252 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: A 273 LEU cc_start: 0.8886 (mm) cc_final: 0.8201 (tp) REVERT: A 279 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8370 (pp) REVERT: A 395 ASP cc_start: 0.7986 (t0) cc_final: 0.7511 (t0) REVERT: A 473 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7139 (t80) REVERT: A 728 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7651 (mm) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.0411 time to fit residues: 7.1480 Evaluate side-chains 116 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 279 LEU Chi-restraints excluded: chain A residue 293 HIS 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 593 ILE 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 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 8 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.124414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101499 restraints weight = 12354.348| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.85 r_work: 0.3507 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5732 Z= 0.132 Angle : 0.611 9.059 7798 Z= 0.302 Chirality : 0.044 0.146 920 Planarity : 0.004 0.061 981 Dihedral : 4.231 30.431 742 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.31 % Allowed : 24.88 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -1.62 (0.31), residues: 704 helix: 0.02 (0.34), residues: 231 sheet: -2.58 (0.69), residues: 52 loop : -1.55 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.016 0.002 TYR A 234 PHE 0.014 0.001 PHE A 808 TRP 0.009 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5727) covalent geometry : angle 0.60968 ( 7788) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.38373 ( 10) hydrogen bonds : bond 0.03510 ( 169) hydrogen bonds : angle 4.92502 ( 498) *********************** 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: 27 poor density : 106 time to evaluate : 0.179 Fit side-chains REVERT: A 95 PHE cc_start: 0.8065 (t80) cc_final: 0.7819 (t80) REVERT: A 182 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 231 ASP cc_start: 0.7675 (t0) cc_final: 0.7311 (t0) REVERT: A 245 LYS cc_start: 0.8620 (tttt) cc_final: 0.8246 (mmtm) REVERT: A 252 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: A 273 LEU cc_start: 0.8903 (mm) cc_final: 0.8269 (tp) REVERT: A 371 SER cc_start: 0.9142 (m) cc_final: 0.8434 (t) REVERT: A 395 ASP cc_start: 0.8046 (t0) cc_final: 0.7792 (t0) REVERT: A 473 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7137 (t80) REVERT: A 725 TYR cc_start: 0.7520 (t80) cc_final: 0.7291 (t80) REVERT: A 728 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7673 (mm) REVERT: A 731 ASN cc_start: 0.7655 (p0) cc_final: 0.7320 (p0) outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 0.0400 time to fit residues: 7.1987 Evaluate side-chains 116 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 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 229 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS 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 681 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.121898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098812 restraints weight = 12359.402| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.71 r_work: 0.3465 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5732 Z= 0.191 Angle : 0.690 9.561 7798 Z= 0.338 Chirality : 0.046 0.155 920 Planarity : 0.005 0.060 981 Dihedral : 4.589 32.678 742 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.83 % Allowed : 26.00 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -1.80 (0.31), residues: 704 helix: -0.27 (0.33), residues: 232 sheet: -2.81 (0.65), residues: 60 loop : -1.51 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 643 TYR 0.015 0.002 TYR A 234 PHE 0.024 0.001 PHE A 759 TRP 0.008 0.002 TRP A 539 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5727) covalent geometry : angle 0.68820 ( 7788) SS BOND : bond 0.00574 ( 5) SS BOND : angle 1.67758 ( 10) hydrogen bonds : bond 0.03821 ( 169) hydrogen bonds : angle 5.15231 ( 498) *********************** 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: 24 poor density : 103 time to evaluate : 0.175 Fit side-chains REVERT: A 95 PHE cc_start: 0.8270 (t80) cc_final: 0.8055 (t80) REVERT: A 182 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 231 ASP cc_start: 0.7632 (t0) cc_final: 0.7261 (t0) REVERT: A 245 LYS cc_start: 0.8668 (tttt) cc_final: 0.8322 (mmtm) REVERT: A 252 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: A 273 LEU cc_start: 0.8933 (mm) cc_final: 0.8276 (tp) REVERT: A 395 ASP cc_start: 0.8130 (t0) cc_final: 0.7656 (t70) REVERT: A 473 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7219 (t80) REVERT: A 728 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7714 (mm) REVERT: A 731 ASN cc_start: 0.7748 (p0) cc_final: 0.7453 (p0) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.0409 time to fit residues: 7.2324 Evaluate side-chains 121 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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 442 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 32 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 overall best weight: 0.2574 ------------------------------------------------------------------------------- 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 373 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.125893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103107 restraints weight = 12686.086| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.89 r_work: 0.3536 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5732 Z= 0.114 Angle : 0.639 10.479 7798 Z= 0.309 Chirality : 0.044 0.139 920 Planarity : 0.004 0.061 981 Dihedral : 4.258 27.858 742 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.39 % Allowed : 27.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.31), residues: 704 helix: 0.00 (0.34), residues: 232 sheet: -2.40 (0.82), residues: 40 loop : -1.61 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 643 TYR 0.014 0.002 TYR A 725 PHE 0.014 0.001 PHE A 759 TRP 0.013 0.001 TRP A 474 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5727) covalent geometry : angle 0.63778 ( 7788) SS BOND : bond 0.00280 ( 5) SS BOND : angle 1.22506 ( 10) hydrogen bonds : bond 0.03368 ( 169) hydrogen bonds : angle 4.87492 ( 498) ********************** 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 120 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.128 Fit side-chains REVERT: A 95 PHE cc_start: 0.8196 (t80) cc_final: 0.7927 (t80) REVERT: A 182 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 231 ASP cc_start: 0.7646 (t0) cc_final: 0.7301 (t0) REVERT: A 245 LYS cc_start: 0.8620 (tttt) cc_final: 0.8169 (mmtm) REVERT: A 252 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: A 273 LEU cc_start: 0.8895 (mm) cc_final: 0.8264 (tp) REVERT: A 371 SER cc_start: 0.9067 (m) cc_final: 0.8351 (t) REVERT: A 395 ASP cc_start: 0.8082 (t0) cc_final: 0.7614 (t70) REVERT: A 728 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7644 (mm) REVERT: A 731 ASN cc_start: 0.7673 (p0) cc_final: 0.7357 (p0) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 0.0398 time to fit residues: 6.6501 Evaluate side-chains 112 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 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 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 529 PHE 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 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** 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 = 0.3940 r_free = 0.3940 target = 0.120581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097511 restraints weight = 12301.316| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.75 r_work: 0.3443 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5732 Z= 0.216 Angle : 0.729 10.359 7798 Z= 0.356 Chirality : 0.047 0.152 920 Planarity : 0.005 0.060 981 Dihedral : 4.740 32.426 742 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.51 % Allowed : 26.79 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 aren not related in a simple way. whole: -1.84 (0.31), residues: 704 helix: -0.26 (0.33), residues: 232 sheet: -2.93 (0.63), residues: 61 loop : -1.54 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 604 TYR 0.017 0.002 TYR A 234 PHE 0.022 0.002 PHE A 706 TRP 0.010 0.002 TRP A 602 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 5727) covalent geometry : angle 0.72615 ( 7788) SS BOND : bond 0.00604 ( 5) SS BOND : angle 1.87430 ( 10) hydrogen bonds : bond 0.03932 ( 169) hydrogen bonds : angle 5.24449 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1169.61 seconds wall clock time: 20 minutes 42.31 seconds (1242.31 seconds total)