Starting phenix.real_space_refine on Wed Oct 9 13:31:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdg_43149/10_2024/8vdg_43149.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdg_43149/10_2024/8vdg_43149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdg_43149/10_2024/8vdg_43149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdg_43149/10_2024/8vdg_43149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdg_43149/10_2024/8vdg_43149.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdg_43149/10_2024/8vdg_43149.cif" } resolution = 3.35 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1653 2.51 5 N 427 2.21 5 O 489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 2583 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 811 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain breaks: 4 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 2.60, per 1000 atoms: 1.01 Number of scatterers: 2583 At special positions: 0 Unit cell: (55.1, 59.45, 94.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 489 8.00 N 427 7.00 C 1653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 715 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 323.1 milliseconds 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 606 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 29.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.590A pdb=" N VAL A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.517A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.780A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.963A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.540A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.869A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 19 through 20 111 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 803 1.34 - 1.46: 654 1.46 - 1.58: 1162 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 2639 Sorted by residual: bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.461 1.490 -0.028 9.20e-03 1.18e+04 9.53e+00 bond pdb=" N VAL K 3 " pdb=" CA VAL K 3 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.42e+00 bond pdb=" N GLU K 17 " pdb=" CA GLU K 17 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.63e+00 bond pdb=" N ASP K 18 " pdb=" CA ASP K 18 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.85e+00 bond pdb=" N LEU K 13 " pdb=" CA LEU K 13 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.67e+00 ... (remaining 2634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 3439 1.96 - 3.92: 106 3.92 - 5.88: 12 5.88 - 7.83: 4 7.83 - 9.79: 1 Bond angle restraints: 3562 Sorted by residual: angle pdb=" N ILE H 53 " pdb=" CA ILE H 53 " pdb=" C ILE H 53 " ideal model delta sigma weight residual 109.34 102.26 7.08 2.08e+00 2.31e-01 1.16e+01 angle pdb=" CB MET A 665 " pdb=" CG MET A 665 " pdb=" SD MET A 665 " ideal model delta sigma weight residual 112.70 122.49 -9.79 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ASP K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA THR K 5 " pdb=" CB THR K 5 " pdb=" OG1 THR K 5 " ideal model delta sigma weight residual 109.60 104.99 4.61 1.50e+00 4.44e-01 9.43e+00 angle pdb=" CA GLN K 6 " pdb=" C GLN K 6 " pdb=" O GLN K 6 " ideal model delta sigma weight residual 121.58 118.26 3.32 1.12e+00 7.97e-01 8.80e+00 ... (remaining 3557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 1408 15.66 - 31.32: 107 31.32 - 46.97: 41 46.97 - 62.63: 9 62.63 - 78.29: 3 Dihedral angle restraints: 1568 sinusoidal: 634 harmonic: 934 Sorted by residual: dihedral pdb=" CA MET A 665 " pdb=" C MET A 665 " pdb=" N LYS A 666 " pdb=" CA LYS A 666 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.05 -59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN K 6 " pdb=" CA GLN K 6 " pdb=" CB GLN K 6 " pdb=" CG GLN K 6 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 1565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 273 0.045 - 0.090: 83 0.090 - 0.134: 25 0.134 - 0.179: 7 0.179 - 0.224: 3 Chirality restraints: 391 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 388 not shown) Planarity restraints: 442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 67 " 0.001 2.00e-02 2.50e+03 1.97e-02 6.82e+00 pdb=" CG PHE H 67 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE H 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE H 67 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 67 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 96 " -0.010 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP K 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP K 96 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP K 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 96 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 96 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 96 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 96 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO H 97 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " -0.023 5.00e-02 4.00e+02 ... (remaining 439 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 645 2.80 - 3.32: 2132 3.32 - 3.85: 4378 3.85 - 4.37: 4955 4.37 - 4.90: 9045 Nonbonded interactions: 21155 Sorted by model distance: nonbonded pdb=" OE1 GLU H 33 " pdb=" OH TYR H 50 " model vdw 2.274 3.040 nonbonded pdb=" O TYR K 49 " pdb=" OH TYR K 91 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 680 " pdb=" OH TYR A 707 " model vdw 2.310 3.040 nonbonded pdb=" O ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.332 3.040 nonbonded pdb=" NH1 ARG K 54 " pdb=" O ILE K 58 " model vdw 2.379 3.120 ... (remaining 21150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.006 0.058 2639 Z= 0.359 Angle : 0.821 9.793 3562 Z= 0.473 Chirality : 0.051 0.224 391 Planarity : 0.006 0.042 442 Dihedral : 13.860 78.288 953 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.56 (0.45), residues: 309 helix: -0.56 (0.43), residues: 75 sheet: -1.18 (0.59), residues: 92 loop : -1.05 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 96 HIS 0.004 0.002 HIS A 663 PHE 0.034 0.003 PHE H 67 TYR 0.017 0.003 TYR A 586 ARG 0.005 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 658 GLU cc_start: 0.8161 (tt0) cc_final: 0.6992 (mp0) REVERT: A 665 MET cc_start: 0.7804 (mmp) cc_final: 0.7381 (mmp) REVERT: K 52 SER cc_start: 0.8175 (p) cc_final: 0.7849 (m) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.2499 time to fit residues: 10.1898 Evaluate side-chains 29 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2639 Z= 0.242 Angle : 0.584 11.579 3562 Z= 0.297 Chirality : 0.041 0.141 391 Planarity : 0.004 0.031 442 Dihedral : 4.125 13.837 343 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.17 (0.48), residues: 309 helix: 1.83 (0.51), residues: 77 sheet: -1.13 (0.53), residues: 100 loop : -0.28 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.012 0.002 PHE A 662 TYR 0.013 0.002 TYR K 91 ARG 0.005 0.001 ARG H 100B *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 658 GLU cc_start: 0.8287 (tt0) cc_final: 0.7124 (mp0) REVERT: A 665 MET cc_start: 0.7954 (mmp) cc_final: 0.7613 (mmp) REVERT: K 52 SER cc_start: 0.8326 (p) cc_final: 0.8125 (m) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2755 time to fit residues: 10.2139 Evaluate side-chains 29 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7837 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2639 Z= 0.189 Angle : 0.501 9.063 3562 Z= 0.255 Chirality : 0.039 0.143 391 Planarity : 0.003 0.032 442 Dihedral : 3.985 12.993 343 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.70 % Allowed : 9.51 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.35 (0.49), residues: 309 helix: 2.75 (0.51), residues: 77 sheet: -1.05 (0.53), residues: 107 loop : -0.02 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 79 HIS 0.003 0.001 HIS A 663 PHE 0.009 0.001 PHE A 662 TYR 0.015 0.002 TYR K 91 ARG 0.003 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.298 Fit side-chains REVERT: A 665 MET cc_start: 0.7965 (mmp) cc_final: 0.7446 (mmp) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1653 time to fit residues: 5.7075 Evaluate side-chains 27 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2639 Z= 0.185 Angle : 0.498 8.334 3562 Z= 0.249 Chirality : 0.039 0.141 391 Planarity : 0.003 0.030 442 Dihedral : 3.822 12.791 343 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.76 % Allowed : 10.56 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.67 (0.50), residues: 309 helix: 3.32 (0.51), residues: 77 sheet: -0.89 (0.53), residues: 107 loop : -0.03 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 79 HIS 0.003 0.001 HIS A 663 PHE 0.009 0.001 PHE H 67 TYR 0.013 0.002 TYR K 91 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.303 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.2138 time to fit residues: 7.7503 Evaluate side-chains 30 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.0970 chunk 5 optimal weight: 0.3980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2639 Z= 0.145 Angle : 0.443 6.867 3562 Z= 0.226 Chirality : 0.037 0.141 391 Planarity : 0.003 0.030 442 Dihedral : 3.605 12.296 343 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.41 % Allowed : 10.56 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.93 (0.50), residues: 309 helix: 3.79 (0.50), residues: 76 sheet: -0.75 (0.54), residues: 107 loop : -0.02 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 79 HIS 0.002 0.001 HIS A 663 PHE 0.007 0.001 PHE A 662 TYR 0.012 0.001 TYR K 91 ARG 0.002 0.000 ARG H 100B *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.310 Fit side-chains REVERT: K 50 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7134 (t70) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.1814 time to fit residues: 5.8148 Evaluate side-chains 26 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2639 Z= 0.200 Angle : 0.476 6.975 3562 Z= 0.244 Chirality : 0.038 0.141 391 Planarity : 0.003 0.027 442 Dihedral : 3.750 12.728 343 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 10.56 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.90 (0.50), residues: 309 helix: 3.70 (0.50), residues: 77 sheet: -0.71 (0.53), residues: 107 loop : -0.08 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.003 0.002 HIS A 663 PHE 0.009 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.334 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.2583 time to fit residues: 7.9254 Evaluate side-chains 28 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2639 Z= 0.172 Angle : 0.466 6.878 3562 Z= 0.237 Chirality : 0.038 0.141 391 Planarity : 0.003 0.027 442 Dihedral : 3.635 12.330 343 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.11 % Allowed : 12.32 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.01 (0.50), residues: 309 helix: 3.79 (0.51), residues: 77 sheet: -0.60 (0.55), residues: 107 loop : -0.06 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.003 0.001 HIS A 663 PHE 0.007 0.001 PHE A 662 TYR 0.012 0.001 TYR K 91 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.315 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.1825 time to fit residues: 5.8149 Evaluate side-chains 25 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2639 Z= 0.190 Angle : 0.486 7.008 3562 Z= 0.247 Chirality : 0.039 0.169 391 Planarity : 0.003 0.026 442 Dihedral : 3.643 12.313 343 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.11 % Allowed : 11.62 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.04 (0.51), residues: 309 helix: 3.78 (0.51), residues: 77 sheet: -0.57 (0.56), residues: 107 loop : -0.02 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.003 0.001 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.011 0.001 TYR K 91 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.318 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.1798 time to fit residues: 5.7391 Evaluate side-chains 26 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.7905 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2639 Z= 0.201 Angle : 0.479 6.290 3562 Z= 0.246 Chirality : 0.039 0.172 391 Planarity : 0.003 0.026 442 Dihedral : 3.699 12.919 343 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.76 % Allowed : 11.62 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.00 (0.51), residues: 309 helix: 3.76 (0.51), residues: 77 sheet: -0.64 (0.56), residues: 107 loop : -0.02 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.286 Fit side-chains REVERT: K 105 GLU cc_start: 0.7505 (pt0) cc_final: 0.7268 (pt0) outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 0.2076 time to fit residues: 7.3505 Evaluate side-chains 29 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 1 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: 0.7933 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2639 Z= 0.238 Angle : 0.507 6.809 3562 Z= 0.261 Chirality : 0.040 0.175 391 Planarity : 0.003 0.025 442 Dihedral : 3.807 13.470 343 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 13.03 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.88 (0.51), residues: 309 helix: 3.67 (0.50), residues: 77 sheet: -0.72 (0.56), residues: 107 loop : -0.08 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 96 HIS 0.004 0.002 HIS A 663 PHE 0.009 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.002 0.000 ARG K 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.293 Fit side-chains REVERT: H 12 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (m) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.2089 time to fit residues: 7.4862 Evaluate side-chains 30 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.153793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137036 restraints weight = 2898.536| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.62 r_work: 0.3438 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2639 Z= 0.238 Angle : 0.519 6.680 3562 Z= 0.264 Chirality : 0.040 0.170 391 Planarity : 0.003 0.025 442 Dihedral : 3.828 13.697 343 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 13.03 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.87 (0.51), residues: 309 helix: 3.65 (0.50), residues: 77 sheet: -0.72 (0.56), residues: 107 loop : -0.10 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.002 0.000 ARG K 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1315.10 seconds wall clock time: 25 minutes 59.74 seconds (1559.74 seconds total)