Starting phenix.real_space_refine on Thu Jul 24 09:33:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e28_27828/07_2025/8e28_27828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e28_27828/07_2025/8e28_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2025/8e28_27828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2025/8e28_27828.map" model { file = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2025/8e28_27828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e28_27828/07_2025/8e28_27828.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.48, per 1000 atoms: 0.77 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: 1.41 Conformation dependent library (CDL) restraints added in 789.5 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: 2.06 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: 1.95 Time building geometry restraints manager: 1.66 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: 1.780 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (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 TRP 0.017 0.002 TRP A 468 HIS 0.010 0.002 HIS A 610 PHE 0.039 0.003 PHE A 80 TYR 0.037 0.002 TYR A 689 ARG 0.017 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.12497 ( 216) hydrogen bonds : angle 5.71008 ( 612) covalent geometry : bond 0.00395 ( 5937) covalent geometry : angle 0.83152 ( 8097) *********************** 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 : 0.749 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: 0.2219 time to fit residues: 18.9124 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 : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.133475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.104855 restraints weight = 7087.542| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.92 r_work: 0.3078 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1012 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= 0.137 Angle : 0.530 5.777 8097 Z= 0.274 Chirality : 0.042 0.152 928 Planarity : 0.005 0.054 997 Dihedral : 11.587 73.576 984 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.49 % Allowed : 7.08 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 684 helix: 0.02 (0.36), residues: 210 sheet: -0.21 (0.42), residues: 160 loop : -1.47 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.003 0.001 HIS A 571 PHE 0.015 0.002 PHE A 464 TYR 0.013 0.001 TYR A 674 ARG 0.006 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 216) hydrogen bonds : angle 4.51990 ( 612) covalent geometry : bond 0.00328 ( 5937) covalent geometry : angle 0.53043 ( 8097) *********************** 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: 3 poor density : 56 time to evaluate : 0.602 Fit side-chains REVERT: A 51 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7014 (pt0) REVERT: A 334 GLU cc_start: 0.8380 (tt0) cc_final: 0.8114 (tt0) REVERT: A 511 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7968 (tttm) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.2271 time to fit residues: 16.5635 Evaluate side-chains 54 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS 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 15 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.131211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103609 restraints weight = 7133.867| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.83 r_work: 0.3029 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5937 Z= 0.192 Angle : 0.570 5.766 8097 Z= 0.291 Chirality : 0.044 0.149 928 Planarity : 0.005 0.047 997 Dihedral : 11.563 73.662 984 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.98 % Allowed : 12.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.31), residues: 684 helix: 0.31 (0.37), residues: 204 sheet: 0.14 (0.43), residues: 153 loop : -1.43 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 468 HIS 0.004 0.001 HIS A 610 PHE 0.015 0.002 PHE A 481 TYR 0.011 0.002 TYR A 340 ARG 0.010 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.06043 ( 216) hydrogen bonds : angle 4.55971 ( 612) covalent geometry : bond 0.00466 ( 5937) covalent geometry : angle 0.56951 ( 8097) *********************** 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 67 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.640 Fit side-chains REVERT: A 51 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7199 (pt0) REVERT: A 334 GLU cc_start: 0.8468 (tt0) cc_final: 0.8081 (tt0) REVERT: A 628 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5612 (mtt) REVERT: A 737 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: A 764 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6249 (mp0) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.2333 time to fit residues: 17.9690 Evaluate side-chains 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.130123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102323 restraints weight = 7265.769| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.84 r_work: 0.3006 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5937 Z= 0.227 Angle : 0.588 5.874 8097 Z= 0.301 Chirality : 0.045 0.151 928 Planarity : 0.005 0.050 997 Dihedral : 11.637 73.712 984 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.14 % Allowed : 16.14 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 684 helix: 0.33 (0.37), residues: 204 sheet: 0.38 (0.44), residues: 145 loop : -1.49 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 468 HIS 0.004 0.001 HIS A 610 PHE 0.017 0.002 PHE A 481 TYR 0.012 0.002 TYR A 340 ARG 0.008 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.06327 ( 216) hydrogen bonds : angle 4.59191 ( 612) covalent geometry : bond 0.00557 ( 5937) covalent geometry : angle 0.58797 ( 8097) *********************** 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 64 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.613 Fit side-chains REVERT: A 51 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7219 (pt0) REVERT: A 334 GLU cc_start: 0.8527 (tt0) cc_final: 0.8096 (tt0) REVERT: A 628 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5539 (mtt) REVERT: A 737 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: A 764 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6183 (mp0) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.2039 time to fit residues: 15.1994 Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 622 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.133836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105297 restraints weight = 7093.666| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.91 r_work: 0.2999 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1553 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= 0.087 Angle : 0.464 5.333 8097 Z= 0.240 Chirality : 0.040 0.140 928 Planarity : 0.004 0.034 997 Dihedral : 11.385 73.676 984 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.65 % Allowed : 17.79 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.32), residues: 684 helix: 0.97 (0.38), residues: 204 sheet: 0.61 (0.44), residues: 156 loop : -1.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 PHE 0.010 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.005 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 216) hydrogen bonds : angle 4.20250 ( 612) covalent geometry : bond 0.00189 ( 5937) covalent geometry : angle 0.46419 ( 8097) *********************** 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 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.591 Fit side-chains REVERT: A 51 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7021 (pt0) REVERT: A 334 GLU cc_start: 0.8466 (tt0) cc_final: 0.8020 (tt0) REVERT: A 352 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 628 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5631 (mtt) REVERT: A 764 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.5870 (mp0) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.2117 time to fit residues: 15.5955 Evaluate side-chains 58 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 628 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.130729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101874 restraints weight = 7136.758| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.93 r_work: 0.2957 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1645 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= 0.139 Angle : 0.498 5.302 8097 Z= 0.254 Chirality : 0.042 0.141 928 Planarity : 0.004 0.034 997 Dihedral : 11.352 73.619 984 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.98 % Allowed : 18.62 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.32), residues: 684 helix: 0.94 (0.37), residues: 204 sheet: 0.34 (0.43), residues: 160 loop : -1.10 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 PHE 0.013 0.001 PHE A 481 TYR 0.010 0.001 TYR A 653 ARG 0.006 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 216) hydrogen bonds : angle 4.25978 ( 612) covalent geometry : bond 0.00334 ( 5937) covalent geometry : angle 0.49770 ( 8097) *********************** 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: 12 poor density : 52 time to evaluate : 0.668 Fit side-chains REVERT: A 51 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7050 (pt0) REVERT: A 334 GLU cc_start: 0.8512 (tt0) cc_final: 0.8113 (tt0) REVERT: A 352 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8184 (mp) REVERT: A 628 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5645 (mtt) REVERT: A 657 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7465 (mmt90) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.2397 time to fit residues: 18.0079 Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 657 ARG Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.131786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102966 restraints weight = 7207.365| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.93 r_work: 0.2958 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1654 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 : 0.485 5.292 8097 Z= 0.248 Chirality : 0.041 0.138 928 Planarity : 0.004 0.035 997 Dihedral : 11.327 73.622 984 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.47 % Allowed : 18.45 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.33), residues: 684 helix: 1.00 (0.37), residues: 204 sheet: 0.33 (0.43), residues: 161 loop : -1.05 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 PHE 0.012 0.001 PHE A 481 TYR 0.010 0.001 TYR A 653 ARG 0.007 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 216) hydrogen bonds : angle 4.21854 ( 612) covalent geometry : bond 0.00289 ( 5937) covalent geometry : angle 0.48483 ( 8097) *********************** 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: 15 poor density : 51 time to evaluate : 0.604 Fit side-chains REVERT: A 51 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7013 (pt0) REVERT: A 334 GLU cc_start: 0.8474 (tt0) cc_final: 0.8054 (tt0) REVERT: A 352 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 628 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5640 (mtt) REVERT: A 657 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7522 (mmt90) REVERT: A 764 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6058 (mp0) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.2303 time to fit residues: 17.6149 Evaluate side-chains 62 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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 19 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.132660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104074 restraints weight = 7136.902| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.92 r_work: 0.2986 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1682 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= 0.106 Angle : 0.470 5.296 8097 Z= 0.241 Chirality : 0.041 0.134 928 Planarity : 0.004 0.034 997 Dihedral : 11.262 73.609 984 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.31 % Allowed : 18.62 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.33), residues: 684 helix: 1.14 (0.37), residues: 204 sheet: 0.67 (0.44), residues: 157 loop : -1.10 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.012 0.001 PHE A 648 TYR 0.009 0.001 TYR A 653 ARG 0.010 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 216) hydrogen bonds : angle 4.12110 ( 612) covalent geometry : bond 0.00251 ( 5937) covalent geometry : angle 0.46971 ( 8097) *********************** 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 63 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.606 Fit side-chains REVERT: A 51 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7020 (pt0) REVERT: A 334 GLU cc_start: 0.8476 (tt0) cc_final: 0.8070 (tt0) REVERT: A 352 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 628 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5677 (mtt) REVERT: A 657 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7413 (mmt90) REVERT: A 764 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.5992 (mp0) outliers start: 14 outliers final: 9 residues processed: 58 average time/residue: 0.2094 time to fit residues: 15.9504 Evaluate side-chains 61 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 42 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105401 restraints weight = 7139.718| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.92 r_work: 0.3012 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1698 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= 0.088 Angle : 0.447 5.252 8097 Z= 0.230 Chirality : 0.040 0.133 928 Planarity : 0.004 0.032 997 Dihedral : 11.171 73.577 984 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 19.60 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.33), residues: 684 helix: 1.28 (0.38), residues: 204 sheet: 0.75 (0.43), residues: 154 loop : -0.99 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.012 0.001 PHE A 648 TYR 0.008 0.001 TYR A 674 ARG 0.006 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 216) hydrogen bonds : angle 4.03305 ( 612) covalent geometry : bond 0.00201 ( 5937) covalent geometry : angle 0.44742 ( 8097) *********************** 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 60 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.675 Fit side-chains REVERT: A 51 GLU cc_start: 0.8021 (mm-30) cc_final: 0.6975 (pt0) REVERT: A 334 GLU cc_start: 0.8482 (tt0) cc_final: 0.8076 (tt0) REVERT: A 352 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 764 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: A 825 MET cc_start: 0.5389 (mmm) cc_final: 0.5186 (mmm) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.1810 time to fit residues: 14.3123 Evaluate side-chains 56 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 741 ASP 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 52 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.129685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100677 restraints weight = 7255.143| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.94 r_work: 0.2923 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5937 Z= 0.193 Angle : 0.544 5.549 8097 Z= 0.278 Chirality : 0.044 0.142 928 Planarity : 0.005 0.037 997 Dihedral : 11.316 73.587 984 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.98 % Allowed : 19.44 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.32), residues: 684 helix: 0.84 (0.37), residues: 205 sheet: 0.31 (0.43), residues: 161 loop : -1.08 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 468 HIS 0.003 0.001 HIS A 571 PHE 0.017 0.002 PHE A 481 TYR 0.012 0.002 TYR A 653 ARG 0.005 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.05842 ( 216) hydrogen bonds : angle 4.35745 ( 612) covalent geometry : bond 0.00470 ( 5937) covalent geometry : angle 0.54445 ( 8097) ********************** 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: 12 poor density : 48 time to evaluate : 0.609 Fit side-chains REVERT: A 51 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7054 (pt0) REVERT: A 334 GLU cc_start: 0.8540 (tt0) cc_final: 0.8109 (tt0) REVERT: A 352 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 657 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7507 (mmt90) REVERT: A 764 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6251 (mp0) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.2249 time to fit residues: 16.1361 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 : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.132276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103591 restraints weight = 7190.227| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.93 r_work: 0.2975 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1768 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= 0.105 Angle : 0.474 5.225 8097 Z= 0.244 Chirality : 0.041 0.135 928 Planarity : 0.004 0.039 997 Dihedral : 11.233 73.623 984 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.81 % Allowed : 19.44 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.33), residues: 684 helix: 1.12 (0.37), residues: 205 sheet: 0.35 (0.43), residues: 161 loop : -0.97 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.013 0.001 PHE A 648 TYR 0.010 0.001 TYR A 653 ARG 0.006 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 216) hydrogen bonds : angle 4.17261 ( 612) covalent geometry : bond 0.00246 ( 5937) covalent geometry : angle 0.47431 ( 8097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.26 seconds wall clock time: 65 minutes 13.01 seconds (3913.01 seconds total)