Starting phenix.real_space_refine on Sun Mar 10 19:32:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/03_2024/7zz0_15030_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/03_2024/7zz0_15030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/03_2024/7zz0_15030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/03_2024/7zz0_15030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/03_2024/7zz0_15030_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/03_2024/7zz0_15030_updated.pdb" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Mg 1 5.21 5 S 19 5.16 5 C 2736 2.51 5 N 731 2.21 5 O 899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A ASP 935": "OD1" <-> "OD2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4387 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4387 Unusual residues: {' MG': 1, ' MN': 1} Classifications: {'peptide': 541, 'undetermined': 2, 'water': 84} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515, None: 86} Not linked: pdbres="GLY A1000 " pdbres=" MG A1201 " Not linked: pdbres=" MG A1201 " pdbres=" MN A1202 " Not linked: pdbres=" MN A1202 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " Not linked: pdbres="HOH A1302 " pdbres="HOH A1303 " ... (remaining 81 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.06, per 1000 atoms: 0.70 Number of scatterers: 4387 At special positions: 0 Unit cell: (71.02, 77.38, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 19 16.00 Mg 1 11.99 O 899 8.00 N 731 7.00 C 2736 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: 1.87 Conformation dependent library (CDL) restraints added in 793.9 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 2 sheets defined 51.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.796A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 645 through 657 removed outlier: 4.355A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'A' and resid 740 through 750 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 789 through 809 removed outlier: 3.778A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 806 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Proline residue: A 808 - end of helix Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.975A pdb=" N HIS A 823 " --> pdb=" O VAL A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 839 Processing helix chain 'A' and resid 843 through 859 removed outlier: 3.798A pdb=" N PHE A 846 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP A 847 " --> pdb=" O HIS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 Processing helix chain 'A' and resid 887 through 893 Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 920 through 926 Processing helix chain 'A' and resid 946 through 956 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 994 through 999 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= B, first strand: chain 'A' and resid 728 through 731 removed outlier: 6.145A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 13.139A pdb=" N ARG A 606 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N GLY A 570 " --> pdb=" O ARG A 606 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 480 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: 1.18 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1425 1.34 - 1.46: 976 1.46 - 1.58: 1958 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 4396 Sorted by residual: bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CE KCX A 703 " pdb=" NZ KCX A 703 " ideal model delta sigma weight residual 1.442 1.487 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C LEU A 645 " pdb=" N PRO A 646 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.68e+00 bond pdb=" C ALA A 807 " pdb=" N PRO A 808 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.19e-02 7.06e+03 1.99e+00 bond pdb=" CG ASP A 723 " pdb=" OD1 ASP A 723 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.40e+00 ... (remaining 4391 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.48: 137 106.48 - 113.39: 2332 113.39 - 120.30: 1595 120.30 - 127.21: 1838 127.21 - 134.12: 49 Bond angle restraints: 5951 Sorted by residual: angle pdb=" CA MET A 822 " pdb=" CB MET A 822 " pdb=" CG MET A 822 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CB MET A 822 " pdb=" CG MET A 822 " pdb=" SD MET A 822 " ideal model delta sigma weight residual 112.70 122.33 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C LYS A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta sigma weight residual 121.58 115.57 6.01 1.95e+00 2.63e-01 9.50e+00 angle pdb=" C VAL A 927 " pdb=" CA VAL A 927 " pdb=" CB VAL A 927 " ideal model delta sigma weight residual 110.98 114.52 -3.54 1.37e+00 5.33e-01 6.67e+00 angle pdb=" CA GLN A 749 " pdb=" CB GLN A 749 " pdb=" CG GLN A 749 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.56e+00 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2272 17.56 - 35.11: 269 35.11 - 52.67: 83 52.67 - 70.23: 18 70.23 - 87.78: 4 Dihedral angle restraints: 2646 sinusoidal: 1077 harmonic: 1569 Sorted by residual: dihedral pdb=" CA ARG A 533 " pdb=" C ARG A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE A 918 " pdb=" C PHE A 918 " pdb=" N PRO A 919 " pdb=" CA PRO A 919 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA MET A 705 " pdb=" CB MET A 705 " pdb=" CG MET A 705 " pdb=" SD MET A 705 " ideal model delta sinusoidal sigma weight residual -60.00 -119.93 59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 581 0.070 - 0.139: 62 0.139 - 0.209: 6 0.209 - 0.278: 0 0.278 - 0.348: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CG LEU A 465 " pdb=" CB LEU A 465 " pdb=" CD1 LEU A 465 " pdb=" CD2 LEU A 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 552 " pdb=" CA ILE A 552 " pdb=" CG1 ILE A 552 " pdb=" CG2 ILE A 552 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 866 " pdb=" CA VAL A 866 " pdb=" CG1 VAL A 866 " pdb=" CG2 VAL A 866 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 647 not shown) Planarity restraints: 777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 614 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" CD GLN A 614 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 614 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 614 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 533 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ARG A 533 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 533 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP A 534 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 807 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 808 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 808 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 808 " -0.022 5.00e-02 4.00e+02 ... (remaining 774 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 173 2.70 - 3.25: 4393 3.25 - 3.80: 8117 3.80 - 4.35: 10368 4.35 - 4.90: 16377 Nonbonded interactions: 39428 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.149 2.320 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.157 2.320 nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.167 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1350 " model vdw 2.189 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.225 2.400 ... (remaining 39423 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: 1.090 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: 5.580 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.090 Find NCS groups from input model: 0.120 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 4396 Z= 0.259 Angle : 0.707 9.630 5951 Z= 0.382 Chirality : 0.046 0.348 650 Planarity : 0.004 0.038 777 Dihedral : 16.824 87.784 1642 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.96 % Allowed : 15.47 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.33), residues: 536 helix: -0.06 (0.27), residues: 293 sheet: -0.43 (0.71), residues: 45 loop : -0.14 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 799 HIS 0.004 0.001 HIS A 732 PHE 0.012 0.002 PHE A 879 TYR 0.012 0.001 TYR A 578 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.531 Fit side-chains REVERT: A 880 MET cc_start: 0.8393 (mtp) cc_final: 0.8105 (mtp) outliers start: 9 outliers final: 9 residues processed: 36 average time/residue: 1.2017 time to fit residues: 45.4367 Evaluate side-chains 37 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 882 GLN Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 50.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.9017 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4396 Z= 0.220 Angle : 0.483 5.895 5951 Z= 0.252 Chirality : 0.041 0.170 650 Planarity : 0.004 0.029 777 Dihedral : 7.082 52.089 614 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.96 % Allowed : 14.81 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.34), residues: 536 helix: 0.88 (0.29), residues: 295 sheet: -0.47 (0.70), residues: 45 loop : 0.37 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.010 0.001 PHE A 879 TYR 0.010 0.001 TYR A 775 ARG 0.003 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.594 Fit side-chains REVERT: A 460 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6753 (ttp-110) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 1.2126 time to fit residues: 40.8853 Evaluate side-chains 32 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 50 optimal weight: 0.2980 chunk 55 optimal weight: 50.0000 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.9013 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4396 Z= 0.183 Angle : 0.447 4.994 5951 Z= 0.233 Chirality : 0.039 0.139 650 Planarity : 0.003 0.028 777 Dihedral : 6.415 51.823 605 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.61 % Allowed : 13.94 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 536 helix: 1.17 (0.29), residues: 296 sheet: -0.68 (0.66), residues: 45 loop : 0.49 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.009 0.001 PHE A 879 TYR 0.008 0.001 TYR A 775 ARG 0.002 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 27 time to evaluate : 0.535 Fit side-chains REVERT: A 460 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7034 (ttp-110) outliers start: 12 outliers final: 6 residues processed: 36 average time/residue: 1.1863 time to fit residues: 44.8519 Evaluate side-chains 33 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 50.0000 chunk 42 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 chunk 59 optimal weight: 50.0000 chunk 53 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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: 0.9010 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4396 Z= 0.171 Angle : 0.436 4.960 5951 Z= 0.227 Chirality : 0.039 0.144 650 Planarity : 0.003 0.028 777 Dihedral : 6.350 52.658 605 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.61 % Allowed : 13.94 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.35), residues: 536 helix: 1.32 (0.30), residues: 295 sheet: -0.73 (0.66), residues: 45 loop : 0.55 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.009 0.001 PHE A 879 TYR 0.008 0.001 TYR A 775 ARG 0.002 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 27 time to evaluate : 0.552 Fit side-chains REVERT: A 460 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7011 (ttp-110) outliers start: 12 outliers final: 6 residues processed: 35 average time/residue: 1.3248 time to fit residues: 48.4961 Evaluate side-chains 33 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4396 Z= 0.277 Angle : 0.495 5.079 5951 Z= 0.259 Chirality : 0.042 0.182 650 Planarity : 0.003 0.030 777 Dihedral : 6.672 59.649 605 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 14.38 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.35), residues: 536 helix: 1.28 (0.30), residues: 295 sheet: -0.72 (0.66), residues: 45 loop : 0.57 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.009 0.001 PHE A 605 TYR 0.011 0.001 TYR A 775 ARG 0.005 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 0.527 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 1.1938 time to fit residues: 45.1915 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 50.0000 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 50.0000 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4396 Z= 0.194 Angle : 0.453 5.147 5951 Z= 0.236 Chirality : 0.040 0.172 650 Planarity : 0.003 0.028 777 Dihedral : 6.566 59.705 605 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.40 % Allowed : 15.47 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.35), residues: 536 helix: 1.31 (0.30), residues: 295 sheet: -0.75 (0.68), residues: 45 loop : 0.55 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.008 0.001 PHE A 879 TYR 0.008 0.001 TYR A 775 ARG 0.004 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.537 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 1.2444 time to fit residues: 44.4253 Evaluate side-chains 33 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.9025 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4396 Z= 0.219 Angle : 0.476 6.194 5951 Z= 0.246 Chirality : 0.041 0.221 650 Planarity : 0.003 0.028 777 Dihedral : 6.587 59.696 605 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.83 % Allowed : 14.81 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.36), residues: 536 helix: 1.32 (0.30), residues: 295 sheet: -0.73 (0.69), residues: 45 loop : 0.56 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.009 0.001 PHE A 879 TYR 0.009 0.001 TYR A 775 ARG 0.003 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 0.527 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 35 average time/residue: 1.2195 time to fit residues: 44.8106 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 50.0000 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4396 Z= 0.241 Angle : 0.489 6.488 5951 Z= 0.252 Chirality : 0.041 0.248 650 Planarity : 0.003 0.028 777 Dihedral : 6.606 58.796 605 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 15.47 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.35), residues: 536 helix: 1.28 (0.30), residues: 295 sheet: -0.75 (0.69), residues: 45 loop : 0.56 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.009 0.001 PHE A 605 TYR 0.009 0.001 TYR A 775 ARG 0.003 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.565 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 1.2292 time to fit residues: 42.6973 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.9017 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4396 Z= 0.186 Angle : 0.466 7.270 5951 Z= 0.238 Chirality : 0.040 0.233 650 Planarity : 0.003 0.029 777 Dihedral : 6.525 59.175 605 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 15.47 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.36), residues: 536 helix: 1.32 (0.30), residues: 295 sheet: -0.76 (0.69), residues: 45 loop : 0.59 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.003 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.547 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 34 average time/residue: 1.2513 time to fit residues: 44.8332 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.9018 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4396 Z= 0.190 Angle : 0.474 7.726 5951 Z= 0.241 Chirality : 0.040 0.249 650 Planarity : 0.003 0.029 777 Dihedral : 6.520 59.034 605 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.36), residues: 536 helix: 1.33 (0.30), residues: 295 sheet: -0.79 (0.69), residues: 45 loop : 0.61 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.003 0.000 ARG A 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.545 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 34 average time/residue: 1.2342 time to fit residues: 44.1893 Evaluate side-chains 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.050091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045433 restraints weight = 13955.188| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.52 r_work: 0.2843 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4396 Z= 0.203 Angle : 0.478 7.781 5951 Z= 0.243 Chirality : 0.041 0.248 650 Planarity : 0.003 0.029 777 Dihedral : 6.526 58.932 605 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 15.47 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.36), residues: 536 helix: 1.33 (0.30), residues: 295 sheet: -0.78 (0.69), residues: 45 loop : 0.62 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.003 0.000 ARG A 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.68 seconds wall clock time: 29 minutes 2.62 seconds (1742.62 seconds total)