Starting phenix.real_space_refine on Tue Mar 3 14:08:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e28_27828/03_2026/8e28_27828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e28_27828/03_2026/8e28_27828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e28_27828/03_2026/8e28_27828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e28_27828/03_2026/8e28_27828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e28_27828/03_2026/8e28_27828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e28_27828/03_2026/8e28_27828.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 31 5.16 5 C 3638 2.51 5 N 976 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5789 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5489 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 41, 'TRANS': 648} Chain breaks: 2 Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 8} Time building chain proxies: 1.21, per 1000 atoms: 0.21 Number of scatterers: 5789 At special positions: 0 Unit cell: (79.86, 86.46, 93.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 15 15.00 O 1129 8.00 N 976 7.00 C 3638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 243.5 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 10 sheets defined 32.0% alpha, 23.2% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.438A pdb=" N ASP A 295 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.889A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.765A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.771A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.846A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.598A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.674A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.636A pdb=" N GLN A 685 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 764 removed outlier: 3.557A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.253A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.783A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR A 299 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU A 251 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.424A pdb=" N ARG A 487 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.481A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.430A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796 removed outlier: 3.715A pdb=" N GLY A 776 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 785 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 774 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 802 through 809 removed outlier: 6.713A pdb=" N VAL A 819 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A 805 " --> pdb=" O THR A 817 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 817 " --> pdb=" O HIS A 805 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 807 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 815 " --> pdb=" O PHE A 807 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1626 1.34 - 1.45: 952 1.45 - 1.57: 3283 1.57 - 1.69: 29 1.69 - 1.81: 47 Bond restraints: 5937 Sorted by residual: bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 bond pdb=" C GLU A 330 " pdb=" N PRO A 331 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.76e+00 bond pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 ... (remaining 5932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 7829 2.06 - 4.13: 221 4.13 - 6.19: 36 6.19 - 8.26: 7 8.26 - 10.32: 4 Bond angle restraints: 8097 Sorted by residual: angle pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " ideal model delta sigma weight residual 112.00 120.35 -8.35 2.20e+00 2.07e-01 1.44e+01 angle pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 112.60 118.96 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" N ASN A 391 " pdb=" CA ASN A 391 " pdb=" C ASN A 391 " ideal model delta sigma weight residual 113.17 117.74 -4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" CA LYS A 283 " pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N GLY A 482 " pdb=" CA GLY A 482 " pdb=" C GLY A 482 " ideal model delta sigma weight residual 111.37 115.62 -4.25 1.29e+00 6.01e-01 1.09e+01 ... (remaining 8092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 3067 16.13 - 32.25: 428 32.25 - 48.38: 133 48.38 - 64.51: 41 64.51 - 80.63: 12 Dihedral angle restraints: 3681 sinusoidal: 1657 harmonic: 2024 Sorted by residual: dihedral pdb=" CA PHE A 464 " pdb=" C PHE A 464 " pdb=" N SER A 465 " pdb=" CA SER A 465 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 633 0.043 - 0.086: 212 0.086 - 0.129: 65 0.129 - 0.172: 16 0.172 - 0.215: 2 Chirality restraints: 928 Sorted by residual: chirality pdb=" CB ILE A 856 " pdb=" CA ILE A 856 " pdb=" CG1 ILE A 856 " pdb=" CG2 ILE A 856 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 99 " pdb=" N VAL A 99 " pdb=" C VAL A 99 " pdb=" CB VAL A 99 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 925 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 444 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 445 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 97 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" CG ASP A 97 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 97 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 728 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 729 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.033 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1725 2.83 - 3.35: 4525 3.35 - 3.87: 8908 3.87 - 4.38: 10327 4.38 - 4.90: 18495 Nonbonded interactions: 43980 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 696 " pdb=" OP1 U C 13 " model vdw 2.334 3.040 nonbonded pdb=" OD1 ASP A 288 " pdb=" OH TYR A 296 " model vdw 2.348 3.040 nonbonded pdb=" NH2 ARG A 543 " pdb=" OE2 GLU A 584 " model vdw 2.374 3.120 nonbonded pdb=" NE2 GLN A 827 " pdb=" O GLU A 828 " model vdw 2.379 3.120 ... (remaining 43975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.860 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.260 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5937 Z= 0.193 Angle : 0.832 10.320 8097 Z= 0.443 Chirality : 0.049 0.215 928 Planarity : 0.007 0.062 997 Dihedral : 17.293 80.633 2363 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.30), residues: 684 helix: -1.10 (0.32), residues: 210 sheet: -0.21 (0.42), residues: 163 loop : -1.62 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 231 TYR 0.037 0.002 TYR A 689 PHE 0.039 0.003 PHE A 80 TRP 0.017 0.002 TRP A 468 HIS 0.010 0.002 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5937) covalent geometry : angle 0.83152 ( 8097) hydrogen bonds : bond 0.12497 ( 216) hydrogen bonds : angle 5.71008 ( 612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.175 Fit side-chains REVERT: A 51 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7058 (pt0) REVERT: A 495 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 586 MET cc_start: 0.8192 (mmt) cc_final: 0.7863 (mmt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0545 time to fit residues: 4.6040 Evaluate side-chains 49 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3571 r_free = 0.3571 target = 0.131291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103723 restraints weight = 7098.097| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.83 r_work: 0.3023 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5937 Z= 0.224 Angle : 0.610 6.539 8097 Z= 0.314 Chirality : 0.045 0.155 928 Planarity : 0.006 0.057 997 Dihedral : 11.738 73.610 984 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.82 % Allowed : 9.39 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.30), residues: 684 helix: -0.07 (0.36), residues: 204 sheet: -0.04 (0.43), residues: 156 loop : -1.63 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 231 TYR 0.014 0.002 TYR A 674 PHE 0.018 0.002 PHE A 464 TRP 0.019 0.002 TRP A 468 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 5937) covalent geometry : angle 0.60989 ( 8097) hydrogen bonds : bond 0.06381 ( 216) hydrogen bonds : angle 4.70851 ( 612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.132 Fit side-chains REVERT: A 51 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7234 (pt0) REVERT: A 334 GLU cc_start: 0.8435 (tt0) cc_final: 0.8120 (tt0) REVERT: A 628 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5766 (mtt) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.0870 time to fit residues: 6.1184 Evaluate side-chains 55 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 804 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3558 r_free = 0.3558 target = 0.131377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102668 restraints weight = 7083.580| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.91 r_work: 0.2948 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5937 Z= 0.121 Angle : 0.501 5.294 8097 Z= 0.259 Chirality : 0.042 0.146 928 Planarity : 0.005 0.041 997 Dihedral : 11.525 73.670 984 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.48 % Allowed : 12.85 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.32), residues: 684 helix: 0.50 (0.37), residues: 204 sheet: 0.22 (0.43), residues: 164 loop : -1.38 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.010 0.001 TYR A 653 PHE 0.011 0.001 PHE A 481 TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5937) covalent geometry : angle 0.50117 ( 8097) hydrogen bonds : bond 0.04960 ( 216) hydrogen bonds : angle 4.40388 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.167 Fit side-chains REVERT: A 51 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7043 (pt0) REVERT: A 334 GLU cc_start: 0.8427 (tt0) cc_final: 0.8043 (tt0) REVERT: A 764 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6030 (mp0) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.0959 time to fit residues: 7.1680 Evaluate side-chains 57 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3583 r_free = 0.3583 target = 0.133285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104667 restraints weight = 7092.600| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.91 r_work: 0.3012 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.103 Angle : 0.471 5.251 8097 Z= 0.242 Chirality : 0.041 0.139 928 Planarity : 0.004 0.032 997 Dihedral : 11.352 73.602 984 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.48 % Allowed : 14.66 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.32), residues: 684 helix: 0.89 (0.37), residues: 204 sheet: 0.39 (0.43), residues: 164 loop : -1.21 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 231 TYR 0.009 0.001 TYR A 674 PHE 0.010 0.001 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.003 0.000 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 5937) covalent geometry : angle 0.47061 ( 8097) hydrogen bonds : bond 0.04426 ( 216) hydrogen bonds : angle 4.21431 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.252 Fit side-chains REVERT: A 51 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7055 (pt0) REVERT: A 334 GLU cc_start: 0.8423 (tt0) cc_final: 0.8015 (tt0) REVERT: A 628 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5745 (mtt) REVERT: A 764 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.5928 (mp0) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.0973 time to fit residues: 7.1089 Evaluate side-chains 58 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3577 r_free = 0.3577 target = 0.132852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104090 restraints weight = 7207.112| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.93 r_work: 0.3000 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5937 Z= 0.110 Angle : 0.474 5.177 8097 Z= 0.242 Chirality : 0.041 0.137 928 Planarity : 0.004 0.032 997 Dihedral : 11.273 73.591 984 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.14 % Allowed : 15.65 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.33), residues: 684 helix: 0.99 (0.37), residues: 204 sheet: 0.56 (0.43), residues: 158 loop : -1.10 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 231 TYR 0.009 0.001 TYR A 674 PHE 0.011 0.001 PHE A 648 TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5937) covalent geometry : angle 0.47404 ( 8097) hydrogen bonds : bond 0.04511 ( 216) hydrogen bonds : angle 4.17598 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.203 Fit side-chains REVERT: A 51 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7047 (pt0) REVERT: A 334 GLU cc_start: 0.8487 (tt0) cc_final: 0.8034 (tt0) REVERT: A 352 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 628 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5697 (mtt) REVERT: A 737 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: A 764 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6028 (mp0) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.0913 time to fit residues: 6.8370 Evaluate side-chains 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.131780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103007 restraints weight = 7146.734| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.92 r_work: 0.2964 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5937 Z= 0.131 Angle : 0.488 5.257 8097 Z= 0.250 Chirality : 0.041 0.137 928 Planarity : 0.004 0.033 997 Dihedral : 11.265 73.610 984 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.33), residues: 684 helix: 0.98 (0.37), residues: 204 sheet: 0.58 (0.43), residues: 158 loop : -1.11 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.009 0.001 TYR A 653 PHE 0.013 0.001 PHE A 481 TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5937) covalent geometry : angle 0.48849 ( 8097) hydrogen bonds : bond 0.04900 ( 216) hydrogen bonds : angle 4.21430 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.151 Fit side-chains REVERT: A 51 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7047 (pt0) REVERT: A 334 GLU cc_start: 0.8513 (tt0) cc_final: 0.8122 (tt0) REVERT: A 352 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8179 (mp) REVERT: A 628 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5716 (mtt) REVERT: A 737 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 764 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6072 (mp0) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.0884 time to fit residues: 6.5333 Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3570 r_free = 0.3570 target = 0.132433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103666 restraints weight = 7222.660| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.92 r_work: 0.3053 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5937 Z= 0.112 Angle : 0.473 5.257 8097 Z= 0.242 Chirality : 0.041 0.135 928 Planarity : 0.004 0.032 997 Dihedral : 11.238 73.613 984 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.64 % Allowed : 16.97 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.33), residues: 684 helix: 1.10 (0.37), residues: 204 sheet: 0.69 (0.43), residues: 156 loop : -1.09 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.009 0.001 TYR A 653 PHE 0.011 0.001 PHE A 481 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5937) covalent geometry : angle 0.47278 ( 8097) hydrogen bonds : bond 0.04599 ( 216) hydrogen bonds : angle 4.15597 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.249 Fit side-chains REVERT: A 51 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7022 (pt0) REVERT: A 334 GLU cc_start: 0.8462 (tt0) cc_final: 0.8059 (tt0) REVERT: A 352 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8179 (mp) REVERT: A 657 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7532 (mmt90) REVERT: A 737 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: A 764 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.5978 (mp0) outliers start: 16 outliers final: 10 residues processed: 58 average time/residue: 0.0924 time to fit residues: 6.9433 Evaluate side-chains 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.131832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103044 restraints weight = 7107.820| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.92 r_work: 0.2976 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5937 Z= 0.133 Angle : 0.491 5.275 8097 Z= 0.251 Chirality : 0.041 0.138 928 Planarity : 0.004 0.033 997 Dihedral : 11.242 73.618 984 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.64 % Allowed : 17.46 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.32), residues: 684 helix: 1.06 (0.37), residues: 204 sheet: 0.67 (0.43), residues: 156 loop : -1.13 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.009 0.001 TYR A 653 PHE 0.013 0.001 PHE A 481 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5937) covalent geometry : angle 0.49073 ( 8097) hydrogen bonds : bond 0.04909 ( 216) hydrogen bonds : angle 4.19961 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.167 Fit side-chains REVERT: A 51 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7059 (pt0) REVERT: A 334 GLU cc_start: 0.8480 (tt0) cc_final: 0.8072 (tt0) REVERT: A 352 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 657 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7538 (mmt90) REVERT: A 737 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: A 764 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6087 (mp0) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 0.0887 time to fit residues: 6.9378 Evaluate side-chains 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3579 r_free = 0.3579 target = 0.133130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104428 restraints weight = 7168.219| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.92 r_work: 0.2998 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5937 Z= 0.104 Angle : 0.467 5.256 8097 Z= 0.239 Chirality : 0.040 0.134 928 Planarity : 0.004 0.033 997 Dihedral : 11.205 73.610 984 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.31 % Allowed : 17.63 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.33), residues: 684 helix: 1.21 (0.38), residues: 204 sheet: 0.64 (0.43), residues: 157 loop : -1.05 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 231 TYR 0.009 0.001 TYR A 653 PHE 0.011 0.001 PHE A 648 TRP 0.015 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5937) covalent geometry : angle 0.46650 ( 8097) hydrogen bonds : bond 0.04429 ( 216) hydrogen bonds : angle 4.12754 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.159 Fit side-chains REVERT: A 51 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7035 (pt0) REVERT: A 334 GLU cc_start: 0.8445 (tt0) cc_final: 0.8035 (tt0) REVERT: A 352 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 657 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7501 (mmt90) REVERT: A 737 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: A 764 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.5963 (mp0) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.0949 time to fit residues: 7.2860 Evaluate side-chains 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3608 r_free = 0.3608 target = 0.135467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107496 restraints weight = 7218.326| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.87 r_work: 0.3087 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.085 Angle : 0.443 5.257 8097 Z= 0.227 Chirality : 0.040 0.132 928 Planarity : 0.004 0.032 997 Dihedral : 11.125 73.588 984 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.81 % Allowed : 18.45 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.33), residues: 684 helix: 1.19 (0.37), residues: 210 sheet: 0.60 (0.43), residues: 157 loop : -1.04 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.008 0.001 TYR A 674 PHE 0.012 0.001 PHE A 648 TRP 0.015 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 5937) covalent geometry : angle 0.44254 ( 8097) hydrogen bonds : bond 0.03778 ( 216) hydrogen bonds : angle 4.02202 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.216 Fit side-chains REVERT: A 51 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7020 (pt0) REVERT: A 334 GLU cc_start: 0.8459 (tt0) cc_final: 0.8060 (tt0) REVERT: A 352 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 657 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7393 (mmt90) REVERT: A 764 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.5799 (mp0) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.0902 time to fit residues: 6.6483 Evaluate side-chains 59 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.131855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103069 restraints weight = 7134.792| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.93 r_work: 0.2965 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5937 Z= 0.152 Angle : 0.497 5.277 8097 Z= 0.253 Chirality : 0.042 0.140 928 Planarity : 0.004 0.035 997 Dihedral : 11.162 73.594 984 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 18.45 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.33), residues: 684 helix: 1.14 (0.37), residues: 204 sheet: 0.30 (0.43), residues: 156 loop : -0.89 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.011 0.001 TYR A 653 PHE 0.015 0.001 PHE A 481 TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5937) covalent geometry : angle 0.49658 ( 8097) hydrogen bonds : bond 0.05025 ( 216) hydrogen bonds : angle 4.17546 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.20 seconds wall clock time: 26 minutes 3.63 seconds (1563.63 seconds total)