Starting phenix.real_space_refine on Thu Sep 10 21:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ok7_70555/09_2026/9ok7_70555.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ok7_70555/09_2026/9ok7_70555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ok7_70555/09_2026/9ok7_70555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ok7_70555/09_2026/9ok7_70555.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ok7_70555/09_2026/9ok7_70555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ok7_70555/09_2026/9ok7_70555.map" } resolution = 3.79 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= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 2411 2.51 5 N 676 2.21 5 O 703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3817 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3817 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 4 Time building chain proxies: 1.04, per 1000 atoms: 0.27 Number of scatterers: 3817 At special positions: 0 Unit cell: (57.67, 67.89, 107.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 703 8.00 N 676 7.00 C 2411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 738 " distance=2.03 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: 0.27 Conformation dependent library (CDL) restraints added in 98.9 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 62.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 352 through 362 removed outlier: 4.084A pdb=" N TYR A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.825A pdb=" N ALA A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 387 through 405 removed outlier: 3.913A pdb=" N CYS A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.604A pdb=" N THR A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 435 through 455 removed outlier: 4.117A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.771A pdb=" N LEU A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.550A pdb=" N THR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.816A pdb=" N LEU A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 535 through 535 No H-bonds generated for 'chain 'A' and resid 535 through 535' Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 552 through 564 Processing helix chain 'A' and resid 568 through 586 removed outlier: 3.901A pdb=" N LYS A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 616 through 628 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.919A pdb=" N ARG A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 716 through 725 Processing helix chain 'A' and resid 742 through 754 removed outlier: 4.031A pdb=" N ALA A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 782 through 786 removed outlier: 4.106A pdb=" N ARG A 786 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 removed outlier: 4.461A pdb=" N VAL A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 837 removed outlier: 4.562A pdb=" N MET A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 178 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.35 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: 1285 1.34 - 1.47: 823 1.47 - 1.59: 1739 1.59 - 1.72: 0 1.72 - 1.84: 34 Bond restraints: 3881 Sorted by residual: bond pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 1.808 1.839 -0.031 3.30e-02 9.18e+02 9.06e-01 bond pdb=" CB GLU A 627 " pdb=" CG GLU A 627 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.89e-01 bond pdb=" CA VAL A 680 " pdb=" CB VAL A 680 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.29e-01 bond pdb=" CD GLN A 636 " pdb=" OE1 GLN A 636 " ideal model delta sigma weight residual 1.231 1.218 0.013 1.90e-02 2.77e+03 4.93e-01 bond pdb=" CA ASP A 742 " pdb=" CB ASP A 742 " ideal model delta sigma weight residual 1.541 1.533 0.008 1.20e-02 6.94e+03 4.47e-01 ... (remaining 3876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 5000 1.27 - 2.53: 191 2.53 - 3.80: 40 3.80 - 5.06: 10 5.06 - 6.33: 2 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N ASP A 742 " pdb=" CA ASP A 742 " pdb=" CB ASP A 742 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" NE ARG A 367 " pdb=" CZ ARG A 367 " pdb=" NH2 ARG A 367 " ideal model delta sigma weight residual 119.20 121.39 -2.19 9.00e-01 1.23e+00 5.90e+00 angle pdb=" N LYS A 413 " pdb=" CA LYS A 413 " pdb=" C LYS A 413 " ideal model delta sigma weight residual 114.75 111.92 2.83 1.26e+00 6.30e-01 5.05e+00 angle pdb=" CA CYS A 385 " pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " ideal model delta sigma weight residual 114.40 119.48 -5.08 2.30e+00 1.89e-01 4.88e+00 angle pdb=" NE ARG A 367 " pdb=" CZ ARG A 367 " pdb=" NH1 ARG A 367 " ideal model delta sigma weight residual 121.50 119.35 2.15 1.00e+00 1.00e+00 4.64e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2108 17.93 - 35.86: 230 35.86 - 53.80: 32 53.80 - 71.73: 13 71.73 - 89.66: 4 Dihedral angle restraints: 2387 sinusoidal: 985 harmonic: 1402 Sorted by residual: dihedral pdb=" CA CYS A 677 " pdb=" C CYS A 677 " pdb=" N ARG A 678 " pdb=" CA ARG A 678 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 738 " pdb=" CB CYS A 738 " ideal model delta sinusoidal sigma weight residual 93.00 60.58 32.42 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA VAL A 518 " pdb=" C VAL A 518 " pdb=" N PRO A 519 " pdb=" CA PRO A 519 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 2384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 406 0.030 - 0.059: 136 0.059 - 0.089: 31 0.089 - 0.119: 22 0.119 - 0.148: 4 Chirality restraints: 599 Sorted by residual: chirality pdb=" CA VAL A 518 " pdb=" N VAL A 518 " pdb=" C VAL A 518 " pdb=" CB VAL A 518 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CG LEU A 674 " pdb=" CB LEU A 674 " pdb=" CD1 LEU A 674 " pdb=" CD2 LEU A 674 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 787 " pdb=" N VAL A 787 " pdb=" C VAL A 787 " pdb=" CB VAL A 787 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 596 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 370 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 370 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 370 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 371 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 654 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C MET A 654 " 0.039 2.00e-02 2.50e+03 pdb=" O MET A 654 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 655 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ALA A 632 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE A 633 " -0.011 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 55 2.63 - 3.20: 4026 3.20 - 3.77: 6055 3.77 - 4.33: 7974 4.33 - 4.90: 12725 Nonbonded interactions: 30835 Sorted by model distance: nonbonded pdb=" OG SER A 714 " pdb=" OD2 ASP A 747 " model vdw 2.066 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OH TYR A 372 " model vdw 2.199 3.040 nonbonded pdb=" O GLN A 788 " pdb=" OG1 THR A 789 " model vdw 2.214 3.040 nonbonded pdb=" O GLN A 844 " pdb=" OG1 THR A 845 " model vdw 2.224 3.040 nonbonded pdb=" O GLN A 862 " pdb=" NE ARG A 866 " model vdw 2.260 3.120 ... (remaining 30830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.370 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 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 : 0.003 0.031 3883 Z= 0.123 Angle : 0.608 6.326 5247 Z= 0.327 Chirality : 0.036 0.148 599 Planarity : 0.004 0.037 680 Dihedral : 15.348 89.660 1471 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.67 (0.40), residues: 474 helix: 0.73 (0.33), residues: 260 sheet: None (None), residues: 0 loop : -1.99 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 664 TYR 0.013 0.001 TYR A 372 PHE 0.015 0.002 PHE A 358 TRP 0.008 0.001 TRP A 782 HIS 0.002 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 3881) covalent geometry : angle 0.60310 / 0.32 ( 5243) SS BOND : bond 0.00784 / 0.40 ( 2) SS BOND : angle 2.90039 / 1.68 ( 4) hydrogen bonds : bond 0.12484 / 7.21 ( 178) hydrogen bonds : angle 6.37480 / 4.40 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.149 Fit side-chains REVERT: A 616 ASN cc_start: 0.7132 (m110) cc_final: 0.6706 (m110) REVERT: A 760 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7325 (tt0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0856 time to fit residues: 7.4141 Evaluate side-chains 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.163799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.132223 restraints weight = 7406.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.136762 restraints weight = 4817.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.140020 restraints weight = 3625.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.141979 restraints weight = 2944.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.143696 restraints weight = 2556.172| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.154 Angle : 0.804 9.638 5247 Z= 0.383 Chirality : 0.044 0.179 599 Planarity : 0.005 0.038 680 Dihedral : 4.702 25.216 532 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.96 % Allowed : 13.70 % Favored : 85.34 % 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: -0.82 (0.39), residues: 474 helix: 0.52 (0.32), residues: 273 sheet: None (None), residues: 0 loop : -2.09 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 545 TYR 0.009 0.002 TYR A 623 PHE 0.044 0.003 PHE A 720 TRP 0.031 0.004 TRP A 782 HIS 0.007 0.002 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 3881) covalent geometry : angle 0.80218 / 0.38 ( 5243) SS BOND : bond 0.00732 / 0.38 ( 2) SS BOND : angle 2.12950 / 1.29 ( 4) hydrogen bonds : bond 0.04348 / 2.79 ( 178) hydrogen bonds : angle 5.56373 / 3.86 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.7199 (m110) cc_final: 0.6751 (m110) REVERT: A 760 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7189 (tt0) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.0878 time to fit residues: 7.0480 Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.1980 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.164005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132165 restraints weight = 7240.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.136472 restraints weight = 4755.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.139606 restraints weight = 3585.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.141576 restraints weight = 2926.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.143305 restraints weight = 2542.990| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3883 Z= 0.145 Angle : 0.751 9.224 5247 Z= 0.360 Chirality : 0.042 0.164 599 Planarity : 0.005 0.038 680 Dihedral : 4.672 21.339 532 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.64 % Allowed : 15.38 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.39), residues: 474 helix: 0.37 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -2.09 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 664 TYR 0.011 0.002 TYR A 831 PHE 0.044 0.002 PHE A 720 TRP 0.044 0.004 TRP A 782 HIS 0.005 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 3881) covalent geometry : angle 0.74923 / 0.36 ( 5243) SS BOND : bond 0.00706 / 0.37 ( 2) SS BOND : angle 1.96391 / 1.18 ( 4) hydrogen bonds : bond 0.03982 / 2.58 ( 178) hydrogen bonds : angle 5.47130 / 3.80 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.7236 (m110) cc_final: 0.6549 (m-40) REVERT: A 661 TYR cc_start: 0.8482 (t80) cc_final: 0.8116 (t80) REVERT: A 760 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7156 (tt0) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.0846 time to fit residues: 7.7001 Evaluate side-chains 64 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 45 optimal weight: 0.3980 chunk 34 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.163359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.134332 restraints weight = 7246.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.138913 restraints weight = 4639.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.142125 restraints weight = 3396.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.144227 restraints weight = 2705.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.146098 restraints weight = 2287.591| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3883 Z= 0.132 Angle : 0.762 8.829 5247 Z= 0.362 Chirality : 0.043 0.166 599 Planarity : 0.005 0.036 680 Dihedral : 4.640 20.895 532 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.16 % Allowed : 18.75 % Favored : 79.09 % 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: -0.98 (0.38), residues: 474 helix: 0.36 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -2.12 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 664 TYR 0.031 0.002 TYR A 831 PHE 0.049 0.002 PHE A 720 TRP 0.027 0.002 TRP A 782 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3881) covalent geometry : angle 0.75569 / 0.36 ( 5243) SS BOND : bond 0.00498 / 0.26 ( 2) SS BOND : angle 3.64698 / 1.99 ( 4) hydrogen bonds : bond 0.03665 / 2.42 ( 178) hydrogen bonds : angle 5.33388 / 3.68 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 661 TYR cc_start: 0.8592 (t80) cc_final: 0.8286 (t80) REVERT: A 760 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7119 (tt0) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 0.0733 time to fit residues: 6.0497 Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 HIS A 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.162030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.133188 restraints weight = 7316.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.137603 restraints weight = 4711.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.140769 restraints weight = 3451.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.142950 restraints weight = 2750.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.144745 restraints weight = 2327.101| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3883 Z= 0.135 Angle : 0.778 16.336 5247 Z= 0.360 Chirality : 0.042 0.167 599 Planarity : 0.004 0.036 680 Dihedral : 4.553 19.814 532 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.37 % Allowed : 18.27 % Favored : 78.37 % 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: -0.96 (0.38), residues: 474 helix: 0.39 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -2.13 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 545 TYR 0.030 0.002 TYR A 831 PHE 0.045 0.002 PHE A 720 TRP 0.020 0.002 TRP A 782 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 3881) covalent geometry : angle 0.77368 / 0.36 ( 5243) SS BOND : bond 0.00670 / 0.35 ( 2) SS BOND : angle 3.20395 / 1.82 ( 4) hydrogen bonds : bond 0.03525 / 2.31 ( 178) hydrogen bonds : angle 5.33882 / 3.69 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 661 TYR cc_start: 0.8600 (t80) cc_final: 0.8357 (t80) REVERT: A 760 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7160 (tt0) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.0869 time to fit residues: 7.1354 Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.163650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.132666 restraints weight = 7252.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137220 restraints weight = 4689.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.140475 restraints weight = 3480.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.142618 restraints weight = 2795.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.144500 restraints weight = 2382.848| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3883 Z= 0.125 Angle : 0.780 14.545 5247 Z= 0.359 Chirality : 0.041 0.181 599 Planarity : 0.005 0.041 680 Dihedral : 4.527 20.181 532 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.37 % Allowed : 18.99 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.39), residues: 474 helix: 0.41 (0.31), residues: 275 sheet: None (None), residues: 0 loop : -2.08 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 866 TYR 0.026 0.002 TYR A 831 PHE 0.050 0.002 PHE A 720 TRP 0.016 0.002 TRP A 782 HIS 0.006 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 3881) covalent geometry : angle 0.77688 / 0.36 ( 5243) SS BOND : bond 0.00595 / 0.31 ( 2) SS BOND : angle 2.82555 / 1.63 ( 4) hydrogen bonds : bond 0.03472 / 2.26 ( 178) hydrogen bonds : angle 5.25011 / 3.62 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 TYR cc_start: 0.8567 (t80) cc_final: 0.8342 (t80) REVERT: A 760 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7138 (tt0) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.0845 time to fit residues: 6.8330 Evaluate side-chains 59 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 HIS A 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.163676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.132811 restraints weight = 7228.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.137412 restraints weight = 4656.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.140594 restraints weight = 3452.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.142869 restraints weight = 2786.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.144627 restraints weight = 2377.822| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3883 Z= 0.131 Angle : 0.788 13.983 5247 Z= 0.363 Chirality : 0.042 0.187 599 Planarity : 0.004 0.037 680 Dihedral : 4.497 20.042 532 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.37 % Allowed : 19.23 % Favored : 77.40 % 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: -0.86 (0.39), residues: 474 helix: 0.45 (0.31), residues: 275 sheet: None (None), residues: 0 loop : -2.06 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 866 TYR 0.024 0.002 TYR A 831 PHE 0.051 0.002 PHE A 720 TRP 0.016 0.002 TRP A 782 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 3881) covalent geometry : angle 0.78434 / 0.36 ( 5243) SS BOND : bond 0.00705 / 0.37 ( 2) SS BOND : angle 2.77717 / 1.61 ( 4) hydrogen bonds : bond 0.03474 / 2.30 ( 178) hydrogen bonds : angle 5.21343 / 3.60 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 760 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7147 (tt0) outliers start: 14 outliers final: 12 residues processed: 63 average time/residue: 0.0822 time to fit residues: 6.3481 Evaluate side-chains 61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.162079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.132989 restraints weight = 7382.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.137506 restraints weight = 4717.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.140744 restraints weight = 3451.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.143115 restraints weight = 2741.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.144835 restraints weight = 2301.388| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3883 Z= 0.137 Angle : 0.809 17.279 5247 Z= 0.370 Chirality : 0.043 0.240 599 Planarity : 0.005 0.045 680 Dihedral : 4.514 20.755 532 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.12 % Allowed : 19.71 % Favored : 77.16 % 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: -0.85 (0.39), residues: 474 helix: 0.42 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -2.02 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 866 TYR 0.023 0.002 TYR A 831 PHE 0.041 0.002 PHE A 720 TRP 0.015 0.002 TRP A 782 HIS 0.006 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 3881) covalent geometry : angle 0.80576 / 0.37 ( 5243) SS BOND : bond 0.00716 / 0.37 ( 2) SS BOND : angle 2.76173 / 1.61 ( 4) hydrogen bonds : bond 0.03557 / 2.32 ( 178) hydrogen bonds : angle 5.22321 / 3.61 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 760 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7146 (tt0) outliers start: 13 outliers final: 11 residues processed: 60 average time/residue: 0.0759 time to fit residues: 5.5891 Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 HIS A 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.160044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.130584 restraints weight = 7504.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.134909 restraints weight = 4856.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.138008 restraints weight = 3608.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.140280 restraints weight = 2891.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.142026 restraints weight = 2445.220| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3883 Z= 0.155 Angle : 0.827 17.129 5247 Z= 0.379 Chirality : 0.043 0.222 599 Planarity : 0.005 0.058 680 Dihedral : 4.631 20.854 532 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.37 % Allowed : 19.23 % Favored : 77.40 % 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: -0.96 (0.39), residues: 474 helix: 0.32 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -2.03 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 866 TYR 0.025 0.002 TYR A 831 PHE 0.042 0.002 PHE A 720 TRP 0.016 0.002 TRP A 782 HIS 0.003 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 3881) covalent geometry : angle 0.82342 / 0.38 ( 5243) SS BOND : bond 0.00757 / 0.39 ( 2) SS BOND : angle 2.80938 / 1.63 ( 4) hydrogen bonds : bond 0.03647 / 2.40 ( 178) hydrogen bonds : angle 5.30655 / 3.67 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 760 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7210 (tt0) outliers start: 14 outliers final: 13 residues processed: 61 average time/residue: 0.0771 time to fit residues: 5.7873 Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.162315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.131321 restraints weight = 7312.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.135982 restraints weight = 4693.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.139375 restraints weight = 3476.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.141745 restraints weight = 2779.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.143090 restraints weight = 2352.729| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3883 Z= 0.137 Angle : 0.836 15.992 5247 Z= 0.383 Chirality : 0.043 0.201 599 Planarity : 0.005 0.036 680 Dihedral : 4.585 20.415 532 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.12 % Allowed : 19.23 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.38), residues: 474 helix: 0.34 (0.32), residues: 269 sheet: None (None), residues: 0 loop : -2.13 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 866 TYR 0.023 0.002 TYR A 831 PHE 0.045 0.002 PHE A 720 TRP 0.046 0.005 TRP A 782 HIS 0.003 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 3881) covalent geometry : angle 0.83308 / 0.38 ( 5243) SS BOND : bond 0.00742 / 0.39 ( 2) SS BOND : angle 2.72728 / 1.58 ( 4) hydrogen bonds : bond 0.03685 / 2.39 ( 178) hydrogen bonds : angle 5.27214 / 3.65 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 760 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7157 (tt0) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.0693 time to fit residues: 5.0830 Evaluate side-chains 61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 780 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 HIS A 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.161972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.130611 restraints weight = 7255.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.135198 restraints weight = 4729.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.138462 restraints weight = 3525.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.140787 restraints weight = 2850.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.142407 restraints weight = 2427.791| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3883 Z= 0.141 Angle : 0.859 16.391 5247 Z= 0.391 Chirality : 0.044 0.193 599 Planarity : 0.005 0.036 680 Dihedral : 4.573 20.184 532 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.12 % Allowed : 18.99 % Favored : 77.88 % 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: -1.00 (0.38), residues: 474 helix: 0.37 (0.32), residues: 269 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 866 TYR 0.023 0.002 TYR A 831 PHE 0.046 0.002 PHE A 720 TRP 0.042 0.004 TRP A 782 HIS 0.004 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3881) covalent geometry : angle 0.85592 / 0.39 ( 5243) SS BOND : bond 0.00751 / 0.39 ( 2) SS BOND : angle 2.72727 / 1.58 ( 4) hydrogen bonds : bond 0.03629 / 2.38 ( 178) hydrogen bonds : angle 5.29138 / 3.66 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 866.87 seconds wall clock time: 15 minutes 58.39 seconds (958.39 seconds total)