Starting phenix.real_space_refine on Mon Nov 13 19:25:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/11_2023/7zz0_15030_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/11_2023/7zz0_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_15030/11_2023/7zz0_15030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/11_2023/7zz0_15030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/11_2023/7zz0_15030_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz0_15030/11_2023/7zz0_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-1.21rc1-5144/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: 3.03, per 1000 atoms: 0.69 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: 1.93 Conformation dependent library (CDL) restraints added in 808.2 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: 0.90 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: 1.17 Time building geometry restraints manager: 1.95 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: 1.110 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: 5.430 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.820 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.496 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 36 average time/residue: 1.1943 time to fit residues: 45.0770 Evaluate side-chains 37 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.7440 time to fit residues: 2.2544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9019 moved from start: 0.0814 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= 0.222 Angle : 0.482 5.805 5951 Z= 0.252 Chirality : 0.041 0.178 650 Planarity : 0.004 0.029 777 Dihedral : 4.476 25.416 594 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.83 % Allowed : 13.73 % 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: 0.78 (0.35), residues: 536 helix: 0.91 (0.29), residues: 295 sheet: -0.45 (0.71), residues: 45 loop : 0.38 (0.43), residues: 196 *********************** 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 39 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.560 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 1.2357 time to fit residues: 46.7065 Evaluate side-chains 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1121 time to fit residues: 0.8768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 50.0000 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** A 882 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4396 Z= 0.335 Angle : 0.526 5.409 5951 Z= 0.276 Chirality : 0.043 0.185 650 Planarity : 0.004 0.032 777 Dihedral : 4.649 23.630 594 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.70 % Allowed : 13.29 % Favored : 83.01 % 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: 0.98 (0.35), residues: 536 helix: 1.13 (0.29), residues: 295 sheet: -0.58 (0.66), residues: 43 loop : 0.41 (0.43), residues: 198 *********************** 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 45 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 28 time to evaluate : 0.529 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 41 average time/residue: 1.2368 time to fit residues: 53.0786 Evaluate side-chains 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 27 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0854 time to fit residues: 0.7960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 50.0000 chunk 59 optimal weight: 50.0000 chunk 53 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 882 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4396 Z= 0.132 Angle : 0.435 6.929 5951 Z= 0.224 Chirality : 0.038 0.147 650 Planarity : 0.003 0.028 777 Dihedral : 4.180 20.256 594 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.49 % Allowed : 13.29 % 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: 1.13 (0.35), residues: 536 helix: 1.27 (0.30), residues: 295 sheet: -0.72 (0.67), residues: 45 loop : 0.53 (0.44), residues: 196 *********************** 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 46 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 0.557 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 40 average time/residue: 1.1677 time to fit residues: 49.0314 Evaluate side-chains 37 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.7830 time to fit residues: 2.3326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.9024 moved from start: 0.1063 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= 0.221 Angle : 0.479 7.886 5951 Z= 0.246 Chirality : 0.041 0.202 650 Planarity : 0.003 0.028 777 Dihedral : 4.316 21.722 594 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.83 % Allowed : 14.60 % 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: 1.19 (0.36), residues: 536 helix: 1.31 (0.30), residues: 295 sheet: -0.74 (0.67), residues: 45 loop : 0.59 (0.44), residues: 196 *********************** 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 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 0.523 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 34 average time/residue: 1.1277 time to fit residues: 40.3947 Evaluate side-chains 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0864 time to fit residues: 0.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 50.0000 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 50.0000 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 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: 0.9024 moved from start: 0.1105 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= 0.222 Angle : 0.481 8.414 5951 Z= 0.247 Chirality : 0.041 0.205 650 Planarity : 0.003 0.028 777 Dihedral : 4.323 21.664 594 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.83 % Allowed : 14.60 % 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: 1.20 (0.36), residues: 536 helix: 1.33 (0.30), residues: 295 sheet: -0.78 (0.69), residues: 45 loop : 0.58 (0.44), residues: 196 *********************** 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 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 0.526 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 35 average time/residue: 1.1155 time to fit residues: 41.1161 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0922 time to fit residues: 0.8318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.9022 moved from start: 0.1101 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= 0.209 Angle : 0.482 8.791 5951 Z= 0.245 Chirality : 0.041 0.231 650 Planarity : 0.003 0.028 777 Dihedral : 4.301 21.621 594 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 15.03 % 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: 1.23 (0.36), residues: 536 helix: 1.35 (0.30), residues: 295 sheet: -0.80 (0.69), residues: 45 loop : 0.62 (0.45), residues: 196 *********************** 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 : 0.535 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 34 average time/residue: 1.2399 time to fit residues: 44.2812 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0873 time to fit residues: 0.8490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 0.0570 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 50.0000 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- 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: 0.9042 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4396 Z= 0.305 Angle : 0.536 9.194 5951 Z= 0.273 Chirality : 0.043 0.277 650 Planarity : 0.003 0.029 777 Dihedral : 4.497 23.180 594 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 15.90 % Favored : 81.92 % 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: 1.14 (0.35), residues: 536 helix: 1.26 (0.30), residues: 295 sheet: -0.65 (0.71), residues: 43 loop : 0.52 (0.44), residues: 198 *********************** 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 : 0.528 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 1.1736 time to fit residues: 40.7100 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0850 time to fit residues: 0.7604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.9024 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4396 Z= 0.212 Angle : 0.496 9.546 5951 Z= 0.250 Chirality : 0.041 0.255 650 Planarity : 0.003 0.028 777 Dihedral : 4.347 21.778 594 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 15.90 % Favored : 81.92 % 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: 1.31 (0.30), residues: 295 sheet: -0.79 (0.69), residues: 45 loop : 0.62 (0.44), residues: 196 *********************** 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 35 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.523 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 1.2655 time to fit residues: 43.8751 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0995 time to fit residues: 0.8305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 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: 0.9020 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4396 Z= 0.194 Angle : 0.488 9.341 5951 Z= 0.245 Chirality : 0.041 0.257 650 Planarity : 0.003 0.027 777 Dihedral : 4.297 21.660 594 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.40 % Allowed : 15.90 % Favored : 81.70 % 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: 1.24 (0.36), residues: 536 helix: 1.35 (0.30), residues: 295 sheet: -0.79 (0.69), residues: 45 loop : 0.63 (0.45), residues: 196 ********************** 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 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 27 time to evaluate : 0.559 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 36 average time/residue: 1.2118 time to fit residues: 45.7997 Evaluate side-chains 34 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0893 time to fit residues: 0.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3095 r_free = 0.3095 target = 0.049904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045221 restraints weight = 13894.940| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.52 r_work: 0.2836 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 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 0.024 4396 Z= 0.220 Angle : 0.504 9.179 5951 Z= 0.253 Chirality : 0.041 0.267 650 Planarity : 0.003 0.027 777 Dihedral : 4.324 21.958 594 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 16.12 % Favored : 81.70 % 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: 1.21 (0.36), residues: 536 helix: 1.32 (0.30), residues: 295 sheet: -0.77 (0.69), residues: 45 loop : 0.62 (0.44), residues: 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.09 seconds wall clock time: 28 minutes 41.03 seconds (1721.03 seconds total)