Starting phenix.real_space_refine on Sun Mar 10 22:36:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/03_2024/8b3j_15830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/03_2024/8b3j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/03_2024/8b3j_15830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/03_2024/8b3j_15830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/03_2024/8b3j_15830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/03_2024/8b3j_15830.pdb" } 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 Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 853": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 504": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.36, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 912.5 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: 0.62 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: 1.67 Time building geometry restraints manager: 2.00 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: 99.43 - 106.35: 232 106.35 - 113.26: 3045 113.26 - 120.18: 2038 120.18 - 127.10: 2568 127.10 - 134.01: 91 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 2.440 nonbonded pdb=" OE1 GLU B 131 " pdb=" OG SER B 213 " model vdw 2.162 2.440 nonbonded pdb=" ND2 ASN A 796 " pdb=" OE1 GLU A 799 " model vdw 2.192 2.520 nonbonded pdb=" OG SER C 364 " pdb=" O THR C 366 " model vdw 2.216 2.440 nonbonded pdb=" N GLU A 653 " pdb=" OE1 GLU A 653 " model vdw 2.222 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 8.900 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.683 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: 0.2369 time to fit residues: 21.6097 Evaluate side-chains 68 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5852 Z= 0.220 Angle : 0.560 6.547 7974 Z= 0.293 Chirality : 0.045 0.178 856 Planarity : 0.004 0.033 1048 Dihedral : 4.526 21.405 786 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.43 % Allowed : 18.93 % Favored : 78.64 % 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: -2.59 (0.30), residues: 710 helix: -2.30 (0.58), residues: 66 sheet: -0.77 (0.36), residues: 208 loop : -2.21 (0.27), residues: 436 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 0.009 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 90 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.675 Fit side-chains REVERT: A 812 TYR cc_start: 0.8792 (t80) cc_final: 0.8063 (t80) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 0.2163 time to fit residues: 24.3952 Evaluate side-chains 80 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 832 LEU Chi-restraints excluded: chain A residue 892 VAL 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 35 optimal weight: 0.0040 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 overall best weight: 2.9210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5852 Z= 0.185 Angle : 0.523 6.134 7974 Z= 0.272 Chirality : 0.044 0.169 856 Planarity : 0.004 0.031 1048 Dihedral : 4.255 21.110 786 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.88 % Allowed : 18.61 % Favored : 77.51 % 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: -2.48 (0.30), residues: 710 helix: -2.25 (0.59), residues: 66 sheet: -0.67 (0.36), residues: 210 loop : -2.14 (0.27), 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 0.011 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 101 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.646 Fit side-chains REVERT: A 799 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: A 812 TYR cc_start: 0.8773 (t80) cc_final: 0.8050 (t80) REVERT: A 865 GLU cc_start: 0.7796 (pm20) cc_final: 0.7326 (pm20) outliers start: 24 outliers final: 13 residues processed: 95 average time/residue: 0.2043 time to fit residues: 25.1032 Evaluate side-chains 82 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 799 GLU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 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 378 ILE Chi-restraints excluded: chain C residue 475 ILE 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 47 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN C 606 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5852 Z= 0.394 Angle : 0.639 7.181 7974 Z= 0.335 Chirality : 0.048 0.166 856 Planarity : 0.005 0.040 1048 Dihedral : 4.778 22.885 786 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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: -2.39 (0.30), residues: 710 helix: -2.16 (0.61), residues: 60 sheet: -0.37 (0.37), residues: 197 loop : -2.20 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 453 HIS 0.007 0.001 HIS A 731 PHE 0.017 0.002 PHE C 427 TYR 0.015 0.002 TYR A 663 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 97 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 0.741 Fit side-chains REVERT: A 799 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: A 855 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8553 (tt) REVERT: C 543 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (tt0) outliers start: 29 outliers final: 15 residues processed: 91 average time/residue: 0.1973 time to fit residues: 23.1096 Evaluate side-chains 84 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 799 GLU 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 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL 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 543 GLN 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 0 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5852 Z= 0.216 Angle : 0.556 6.281 7974 Z= 0.290 Chirality : 0.045 0.159 856 Planarity : 0.004 0.030 1048 Dihedral : 4.505 22.162 786 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.24 % Allowed : 20.23 % 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: -2.37 (0.30), residues: 710 helix: -2.04 (0.63), residues: 60 sheet: -0.45 (0.36), residues: 206 loop : -2.18 (0.27), residues: 444 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 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 84 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.686 Fit side-chains REVERT: A 799 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8252 (pt0) REVERT: A 812 TYR cc_start: 0.8812 (t80) cc_final: 0.8098 (t80) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.2138 time to fit residues: 21.8317 Evaluate side-chains 80 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 799 GLU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0947 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= 0.278 Angle : 0.572 6.491 7974 Z= 0.299 Chirality : 0.045 0.156 856 Planarity : 0.004 0.030 1048 Dihedral : 4.527 22.421 786 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.53 % Allowed : 19.26 % 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: -2.39 (0.30), residues: 710 helix: -2.08 (0.62), residues: 60 sheet: -0.44 (0.36), residues: 206 loop : -2.20 (0.27), residues: 444 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 0.012 0.001 PHE C 427 TYR 0.012 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 91 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 0.646 Fit side-chains REVERT: A 799 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: A 855 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8526 (tt) REVERT: B 227 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9112 (tt) outliers start: 28 outliers final: 18 residues processed: 86 average time/residue: 0.1960 time to fit residues: 22.0942 Evaluate side-chains 83 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 799 GLU 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 188 LYS 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 336 VAL 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 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 38 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 40.0000 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5852 Z= 0.368 Angle : 0.623 6.523 7974 Z= 0.325 Chirality : 0.047 0.155 856 Planarity : 0.005 0.034 1048 Dihedral : 4.757 23.056 786 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.37 % Allowed : 19.90 % Favored : 75.73 % 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: -2.40 (0.30), residues: 710 helix: -2.16 (0.61), residues: 60 sheet: -0.23 (0.37), residues: 195 loop : -2.28 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 453 HIS 0.006 0.001 HIS A 731 PHE 0.015 0.002 PHE C 427 TYR 0.015 0.001 TYR A 663 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 88 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 0.780 Fit side-chains REVERT: A 799 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 855 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8525 (tt) REVERT: B 227 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9119 (tt) outliers start: 27 outliers final: 21 residues processed: 83 average time/residue: 0.2049 time to fit residues: 22.1794 Evaluate side-chains 85 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 799 GLU 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 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 212 ILE 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 336 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 443 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0996 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= 0.246 Angle : 0.561 6.626 7974 Z= 0.292 Chirality : 0.045 0.155 856 Planarity : 0.004 0.029 1048 Dihedral : 4.510 22.333 786 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.88 % Allowed : 20.87 % Favored : 75.24 % 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: -2.41 (0.30), residues: 710 helix: -2.17 (0.63), residues: 59 sheet: -0.43 (0.36), residues: 206 loop : -2.21 (0.27), residues: 445 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 402 TYR 0.013 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 87 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 0.686 Fit side-chains REVERT: A 855 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 227 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9125 (tt) outliers start: 24 outliers final: 19 residues processed: 83 average time/residue: 0.2111 time to fit residues: 22.5555 Evaluate side-chains 84 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 VAL 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 443 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 0.0970 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 0.0000 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5852 Z= 0.231 Angle : 0.551 6.492 7974 Z= 0.286 Chirality : 0.044 0.154 856 Planarity : 0.004 0.029 1048 Dihedral : 4.411 22.099 786 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.72 % Allowed : 21.36 % Favored : 74.92 % 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: -2.40 (0.30), residues: 710 helix: -2.16 (0.63), residues: 59 sheet: -0.43 (0.36), residues: 206 loop : -2.20 (0.27), residues: 445 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 0.011 0.001 PHE C 402 TYR 0.012 0.001 TYR B 150 ARG 0.004 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 87 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.655 Fit side-chains REVERT: A 812 TYR cc_start: 0.8800 (t80) cc_final: 0.8277 (t80) REVERT: A 855 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8472 (tt) outliers start: 23 outliers final: 20 residues processed: 83 average time/residue: 0.2107 time to fit residues: 22.4328 Evaluate side-chains 84 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 188 LYS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 VAL 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 443 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 0.0030 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 8 optimal weight: 9.9990 overall best weight: 3.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1172 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= 0.192 Angle : 0.544 10.938 7974 Z= 0.281 Chirality : 0.044 0.155 856 Planarity : 0.004 0.029 1048 Dihedral : 4.257 21.604 786 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.40 % Allowed : 21.52 % Favored : 75.08 % 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: -2.12 (0.63), residues: 59 sheet: -0.40 (0.36), residues: 206 loop : -2.14 (0.27), residues: 445 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 0.011 0.001 PHE C 402 TYR 0.016 0.001 TYR A 777 ARG 0.004 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 87 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.685 Fit side-chains REVERT: A 812 TYR cc_start: 0.8778 (t80) cc_final: 0.8239 (t80) REVERT: A 855 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8454 (tt) outliers start: 21 outliers final: 18 residues processed: 83 average time/residue: 0.2098 time to fit residues: 22.3517 Evaluate side-chains 83 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.094719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.078977 restraints weight = 10028.874| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.22 r_work: 0.2884 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5852 Z= 0.237 Angle : 0.562 10.518 7974 Z= 0.291 Chirality : 0.044 0.153 856 Planarity : 0.004 0.029 1048 Dihedral : 4.338 21.923 786 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.40 % Allowed : 21.68 % Favored : 74.92 % 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: -2.39 (0.30), residues: 710 helix: -2.29 (0.58), residues: 65 sheet: -0.41 (0.36), residues: 206 loop : -2.17 (0.27), residues: 439 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 0.011 0.001 PHE C 402 TYR 0.016 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: 1493.26 seconds wall clock time: 27 minutes 35.35 seconds (1655.35 seconds total)