Starting phenix.real_space_refine on Thu Mar 6 09:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3j_15830/03_2025/8b3j_15830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3j_15830/03_2025/8b3j_15830.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/8b3j_15830/03_2025/8b3j_15830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3j_15830/03_2025/8b3j_15830.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3j_15830/03_2025/8b3j_15830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3j_15830/03_2025/8b3j_15830.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= 0.032 sd= 0.161 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 20 5.16 5 C 3635 2.51 5 N 976 2.21 5 O 1057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5688 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2034 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 24, 'TRANS': 232} Chain: "B" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1456 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 12, 'TRANS': 170} Chain breaks: 1 Chain: "C" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2198 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 262} Time building chain proxies: 4.62, per 1000 atoms: 0.81 Number of scatterers: 5688 At special positions: 0 Unit cell: (108.9, 101.2, 93.5, 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 20 16.00 O 1057 8.00 N 976 7.00 C 3635 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: 2.34 Conformation dependent library (CDL) restraints added in 696.9 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 9.1% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.750A pdb=" N THR A 686 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.636A pdb=" N GLN A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.678A pdb=" N THR B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 388 through 392 Processing helix chain 'C' and resid 441 through 447 removed outlier: 3.520A pdb=" N ALA C 446 " --> pdb=" O PRO C 442 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 640 through 641 removed outlier: 4.295A pdb=" N ASP C 400 " --> pdb=" O TRP C 580 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 582 " --> pdb=" O TYR C 398 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 398 " --> pdb=" O VAL C 582 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 674 through 678 removed outlier: 5.085A pdb=" N ALA A 870 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA A 678 " --> pdb=" O TRP A 868 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP A 868 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 753 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 747 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 361 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 783 through 788 removed outlier: 4.470A pdb=" N ARG A 849 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 772 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 766 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 101 removed outlier: 5.474A pdb=" N ARG B 95 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 252 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET B 97 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 247 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 257 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 134 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 259 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR B 132 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 197 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 101 removed outlier: 5.474A pdb=" N ARG B 95 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 252 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET B 97 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 247 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 257 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 134 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 259 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR B 132 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.407A pdb=" N LYS B 152 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 232 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR B 150 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.761A pdb=" N ARG C 470 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP C 564 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG C 472 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 415 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 561 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 413 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 427 through 428 removed outlier: 3.613A pdb=" N GLY C 437 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 149 hydrogen bonds defined for protein. 381 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: 2.02 Time building geometry restraints manager: 2.65 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: 1864 1.34 - 1.46: 1073 1.46 - 1.57: 2880 1.57 - 1.69: 1 1.69 - 1.80: 34 Bond restraints: 5852 Sorted by residual: bond pdb=" CA GLU A 653 " pdb=" CB GLU A 653 " ideal model delta sigma weight residual 1.528 1.574 -0.046 2.61e-02 1.47e+03 3.05e+00 bond pdb=" CG1 ILE A 697 " pdb=" CD1 ILE A 697 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" C LEU A 669 " pdb=" N VAL A 670 " ideal model delta sigma weight residual 1.338 1.328 0.010 1.01e-02 9.80e+03 9.95e-01 bond pdb=" CB GLU A 653 " pdb=" CG GLU A 653 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.88e-01 bond pdb=" CB ASP A 703 " pdb=" CG ASP A 703 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.23e-01 ... (remaining 5847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7612 1.32 - 2.64: 283 2.64 - 3.96: 64 3.96 - 5.28: 12 5.28 - 6.60: 3 Bond angle restraints: 7974 Sorted by residual: angle pdb=" N SER C 592 " pdb=" CA SER C 592 " pdb=" C SER C 592 " ideal model delta sigma weight residual 110.24 114.72 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" C ALA C 591 " pdb=" N SER C 592 " pdb=" CA SER C 592 " ideal model delta sigma weight residual 120.82 125.31 -4.49 1.47e+00 4.63e-01 9.33e+00 angle pdb=" CA GLU A 653 " pdb=" CB GLU A 653 " pdb=" CG GLU A 653 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.40e+00 angle pdb=" CA PRO A 820 " pdb=" C PRO A 820 " pdb=" O PRO A 820 " ideal model delta sigma weight residual 121.38 119.45 1.93 7.70e-01 1.69e+00 6.28e+00 angle pdb=" N LEU B 230 " pdb=" CA LEU B 230 " pdb=" C LEU B 230 " ideal model delta sigma weight residual 113.12 110.18 2.94 1.25e+00 6.40e-01 5.54e+00 ... (remaining 7969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2980 17.50 - 35.00: 359 35.00 - 52.51: 83 52.51 - 70.01: 12 70.01 - 87.51: 3 Dihedral angle restraints: 3437 sinusoidal: 1367 harmonic: 2070 Sorted by residual: dihedral pdb=" CA LEU A 880 " pdb=" C LEU A 880 " pdb=" N SER A 881 " pdb=" CA SER A 881 " ideal model delta harmonic sigma weight residual 180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER B 213 " pdb=" C SER B 213 " pdb=" N GLU B 214 " pdb=" CA GLU B 214 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU A 832 " pdb=" C LEU A 832 " pdb=" N ARG A 833 " pdb=" CA ARG A 833 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 582 0.041 - 0.081: 191 0.081 - 0.121: 77 0.121 - 0.162: 5 0.162 - 0.202: 1 Chirality restraints: 856 Sorted by residual: chirality pdb=" CA ILE A 697 " pdb=" N ILE A 697 " pdb=" C ILE A 697 " pdb=" CB ILE A 697 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE B 248 " pdb=" N ILE B 248 " pdb=" C ILE B 248 " pdb=" CB ILE B 248 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE C 475 " pdb=" N ILE C 475 " pdb=" C ILE C 475 " pdb=" CB ILE C 475 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 853 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 714 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 715 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 158 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO B 159 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 775 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 776 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 776 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 776 " -0.017 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 195 2.70 - 3.25: 5010 3.25 - 3.80: 7952 3.80 - 4.35: 10703 4.35 - 4.90: 18898 Nonbonded interactions: 42758 Sorted by model distance: nonbonded pdb=" O GLY B 145 " pdb=" OG SER B 194 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLU B 131 " pdb=" OG SER B 213 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN A 796 " pdb=" OE1 GLU A 799 " model vdw 2.192 3.120 nonbonded pdb=" OG SER C 364 " pdb=" O THR C 366 " model vdw 2.216 3.040 nonbonded pdb=" N GLU A 653 " pdb=" OE1 GLU A 653 " model vdw 2.222 3.120 ... (remaining 42753 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: 5.320 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:4.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.005 0.049 5852 Z= 0.313 Angle : 0.630 6.597 7974 Z= 0.337 Chirality : 0.046 0.202 856 Planarity : 0.004 0.038 1048 Dihedral : 15.709 87.512 2111 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.49 (0.30), residues: 710 helix: -2.08 (0.67), residues: 54 sheet: -0.62 (0.37), residues: 194 loop : -2.19 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.015 0.002 PHE C 402 TYR 0.013 0.001 TYR A 663 ARG 0.003 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.603 Fit side-chains REVERT: A 812 TYR cc_start: 0.8801 (t80) cc_final: 0.8053 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2273 time to fit residues: 20.6331 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 20.0000 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.094576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.078385 restraints weight = 9992.589| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.29 r_work: 0.2875 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5852 Z= 0.259 Angle : 0.592 6.817 7974 Z= 0.312 Chirality : 0.046 0.177 856 Planarity : 0.005 0.057 1048 Dihedral : 4.664 21.740 786 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.59 % Allowed : 18.45 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.46 (0.30), residues: 710 helix: -2.19 (0.59), residues: 65 sheet: -0.62 (0.36), residues: 204 loop : -2.14 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 PHE 0.010 0.001 PHE C 427 TYR 0.012 0.001 TYR B 150 ARG 0.001 0.000 ARG C 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.697 Fit side-chains REVERT: A 812 TYR cc_start: 0.8872 (t80) cc_final: 0.8187 (t80) REVERT: B 234 LYS cc_start: 0.8592 (mttm) cc_final: 0.8134 (mmtm) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.2128 time to fit residues: 23.3818 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.077133 restraints weight = 10083.257| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.22 r_work: 0.2852 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5852 Z= 0.352 Angle : 0.625 7.148 7974 Z= 0.329 Chirality : 0.048 0.175 856 Planarity : 0.005 0.051 1048 Dihedral : 4.859 22.787 786 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.37 % Allowed : 18.28 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.49 (0.30), residues: 710 helix: -2.43 (0.57), residues: 66 sheet: -0.57 (0.37), residues: 201 loop : -2.16 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 453 HIS 0.006 0.001 HIS A 731 PHE 0.014 0.002 PHE C 427 TYR 0.014 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.652 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 95 average time/residue: 0.1806 time to fit residues: 22.4789 Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077666 restraints weight = 10226.034| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.24 r_work: 0.2861 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5852 Z= 0.292 Angle : 0.599 6.725 7974 Z= 0.315 Chirality : 0.046 0.165 856 Planarity : 0.005 0.050 1048 Dihedral : 4.713 22.539 786 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.69 % Allowed : 18.12 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.44 (0.30), residues: 710 helix: -2.37 (0.58), residues: 66 sheet: -0.47 (0.37), residues: 201 loop : -2.16 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 PHE 0.011 0.001 PHE C 427 TYR 0.013 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.592 Fit side-chains REVERT: A 855 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 865 GLU cc_start: 0.8044 (pm20) cc_final: 0.7456 (pm20) outliers start: 29 outliers final: 19 residues processed: 97 average time/residue: 0.1887 time to fit residues: 23.8940 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 58 optimal weight: 0.0070 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.080268 restraints weight = 9953.356| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.21 r_work: 0.2906 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5852 Z= 0.187 Angle : 0.549 7.202 7974 Z= 0.286 Chirality : 0.044 0.159 856 Planarity : 0.004 0.037 1048 Dihedral : 4.343 21.650 786 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.07 % Allowed : 19.90 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.34 (0.30), residues: 710 helix: -2.29 (0.59), residues: 66 sheet: -0.41 (0.36), residues: 206 loop : -2.11 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.009 0.001 PHE C 402 TYR 0.012 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.694 Fit side-chains REVERT: A 812 TYR cc_start: 0.8872 (t80) cc_final: 0.8201 (t80) outliers start: 19 outliers final: 17 residues processed: 86 average time/residue: 0.2070 time to fit residues: 22.7834 Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 13 optimal weight: 0.0070 chunk 56 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.078828 restraints weight = 9927.840| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.22 r_work: 0.2880 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5852 Z= 0.261 Angle : 0.584 6.401 7974 Z= 0.305 Chirality : 0.046 0.159 856 Planarity : 0.004 0.039 1048 Dihedral : 4.451 22.134 786 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.69 % Allowed : 18.61 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.36 (0.30), residues: 710 helix: -2.30 (0.58), residues: 66 sheet: -0.40 (0.36), residues: 206 loop : -2.13 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 PHE 0.011 0.001 PHE C 402 TYR 0.013 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.834 Fit side-chains REVERT: A 812 TYR cc_start: 0.8890 (t80) cc_final: 0.8334 (t80) REVERT: A 855 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8525 (tt) outliers start: 29 outliers final: 22 residues processed: 88 average time/residue: 0.1896 time to fit residues: 21.9002 Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079030 restraints weight = 10022.166| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.20 r_work: 0.2884 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5852 Z= 0.252 Angle : 0.579 6.308 7974 Z= 0.303 Chirality : 0.045 0.156 856 Planarity : 0.004 0.038 1048 Dihedral : 4.447 22.083 786 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.53 % Allowed : 19.09 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.36 (0.30), residues: 710 helix: -2.36 (0.58), residues: 66 sheet: -0.52 (0.36), residues: 210 loop : -2.07 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.010 0.001 PHE C 402 TYR 0.013 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.673 Fit side-chains REVERT: A 812 TYR cc_start: 0.8873 (t80) cc_final: 0.8372 (t80) REVERT: A 855 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8508 (tt) outliers start: 28 outliers final: 23 residues processed: 86 average time/residue: 0.1935 time to fit residues: 21.8164 Evaluate side-chains 89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 20.0000 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079908 restraints weight = 9888.920| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.22 r_work: 0.2898 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5852 Z= 0.212 Angle : 0.563 6.707 7974 Z= 0.294 Chirality : 0.045 0.156 856 Planarity : 0.004 0.035 1048 Dihedral : 4.290 21.687 786 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.05 % Allowed : 19.74 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.29 (0.30), residues: 710 helix: -2.35 (0.59), residues: 66 sheet: -0.41 (0.36), residues: 208 loop : -2.04 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.010 0.001 PHE C 402 TYR 0.012 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.684 Fit side-chains REVERT: A 812 TYR cc_start: 0.8863 (t80) cc_final: 0.8328 (t80) REVERT: A 855 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 227 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9132 (tt) outliers start: 25 outliers final: 22 residues processed: 85 average time/residue: 0.1909 time to fit residues: 21.2661 Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080173 restraints weight = 9906.929| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.30 r_work: 0.2893 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5852 Z= 0.179 Angle : 0.554 7.012 7974 Z= 0.290 Chirality : 0.044 0.154 856 Planarity : 0.004 0.031 1048 Dihedral : 4.085 20.814 786 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.56 % Allowed : 20.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.20 (0.30), residues: 710 helix: -2.30 (0.60), residues: 66 sheet: -0.35 (0.36), residues: 208 loop : -1.97 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 580 HIS 0.003 0.001 HIS A 731 PHE 0.009 0.001 PHE C 402 TYR 0.015 0.001 TYR A 777 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.656 Fit side-chains REVERT: A 812 TYR cc_start: 0.8889 (t80) cc_final: 0.8395 (t80) REVERT: A 855 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 227 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9113 (tt) outliers start: 22 outliers final: 19 residues processed: 85 average time/residue: 0.1917 time to fit residues: 21.2508 Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.077111 restraints weight = 10211.988| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.29 r_work: 0.2847 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5852 Z= 0.359 Angle : 0.640 7.366 7974 Z= 0.338 Chirality : 0.047 0.156 856 Planarity : 0.005 0.079 1048 Dihedral : 4.580 22.690 786 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.72 % Allowed : 19.74 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.33 (0.30), residues: 710 helix: -2.45 (0.57), residues: 66 sheet: -0.40 (0.36), residues: 208 loop : -2.08 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 580 HIS 0.006 0.001 HIS A 731 PHE 0.013 0.002 PHE C 493 TYR 0.016 0.002 TYR A 777 ARG 0.003 0.000 ARG B 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.676 Fit side-chains REVERT: A 812 TYR cc_start: 0.8918 (t80) cc_final: 0.8215 (t80) REVERT: A 855 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8537 (tt) REVERT: B 227 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9140 (tt) outliers start: 23 outliers final: 19 residues processed: 81 average time/residue: 0.2033 time to fit residues: 21.1686 Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.079258 restraints weight = 10070.112| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.31 r_work: 0.2879 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5852 Z= 0.206 Angle : 0.570 7.480 7974 Z= 0.300 Chirality : 0.044 0.154 856 Planarity : 0.005 0.067 1048 Dihedral : 4.301 21.615 786 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.56 % Allowed : 20.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.26 (0.30), residues: 710 helix: -2.35 (0.60), residues: 66 sheet: -0.41 (0.36), residues: 210 loop : -2.01 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.009 0.001 PHE C 402 TYR 0.015 0.001 TYR A 777 ARG 0.003 0.000 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.60 seconds wall clock time: 58 minutes 30.29 seconds (3510.29 seconds total)