Starting phenix.real_space_refine on Mon Jan 13 14:27:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdg_43149/01_2025/8vdg_43149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdg_43149/01_2025/8vdg_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/cci-nas-00/data/ceres_data/8vdg_43149/01_2025/8vdg_43149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdg_43149/01_2025/8vdg_43149.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdg_43149/01_2025/8vdg_43149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdg_43149/01_2025/8vdg_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-5571/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: 2.98, per 1000 atoms: 1.15 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: 0.62 Conformation dependent library (CDL) restraints added in 314.2 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: 0.32 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: 0.63 Time building geometry restraints manager: 0.72 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: 1.950 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.580 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.287 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: 0.2333 time to fit residues: 9.4209 Evaluate side-chains 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.157494 restraints weight = 2929.826| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.81 r_work: 0.3610 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 658 GLU cc_start: 0.8437 (tt0) cc_final: 0.7157 (mp0) REVERT: A 665 MET cc_start: 0.8037 (mmp) cc_final: 0.7712 (mmp) REVERT: H 85 GLU cc_start: 0.7694 (pm20) cc_final: 0.7488 (pm20) REVERT: K 52 SER cc_start: 0.8471 (p) cc_final: 0.8253 (m) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2281 time to fit residues: 8.3809 Evaluate side-chains 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.168594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149735 restraints weight = 2979.731| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.79 r_work: 0.3511 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 2639 Z= 0.314 Angle : 0.598 11.120 3562 Z= 0.303 Chirality : 0.042 0.151 391 Planarity : 0.004 0.033 442 Dihedral : 4.373 13.834 343 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.70 % Allowed : 11.27 % 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: -0.03 (0.48), residues: 309 helix: 2.42 (0.51), residues: 77 sheet: -1.26 (0.50), residues: 107 loop : -0.27 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 79 HIS 0.005 0.002 HIS A 663 PHE 0.012 0.002 PHE A 662 TYR 0.016 0.002 TYR K 91 ARG 0.003 0.001 ARG K 61 *********************** 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 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.274 Fit side-chains REVERT: A 665 MET cc_start: 0.8117 (mmp) cc_final: 0.7765 (mmp) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1976 time to fit residues: 6.6215 Evaluate side-chains 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.155071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137245 restraints weight = 2949.769| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.74 r_work: 0.3428 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 2639 Z= 0.267 Angle : 0.542 9.998 3562 Z= 0.276 Chirality : 0.041 0.149 391 Planarity : 0.003 0.028 442 Dihedral : 4.274 14.740 343 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.76 % Allowed : 11.27 % Favored : 86.97 % 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: 0.18 (0.48), residues: 309 helix: 2.85 (0.50), residues: 77 sheet: -1.12 (0.51), residues: 107 loop : -0.36 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.010 0.001 PHE H 67 TYR 0.014 0.002 TYR K 91 ARG 0.002 0.001 ARG K 108 *********************** 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 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.287 Fit side-chains REVERT: A 665 MET cc_start: 0.8012 (mmp) cc_final: 0.7553 (mmp) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1641 time to fit residues: 5.7011 Evaluate side-chains 28 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 0.0020 chunk 2 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139274 restraints weight = 2924.114| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.70 r_work: 0.3446 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2639 Z= 0.196 Angle : 0.497 8.898 3562 Z= 0.251 Chirality : 0.039 0.148 391 Planarity : 0.003 0.028 442 Dihedral : 3.992 13.706 343 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.76 % Allowed : 11.97 % 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: 0.51 (0.49), residues: 309 helix: 3.25 (0.51), residues: 77 sheet: -0.94 (0.53), residues: 107 loop : -0.24 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 79 HIS 0.003 0.002 HIS A 663 PHE 0.008 0.001 PHE H 67 TYR 0.013 0.002 TYR K 91 ARG 0.002 0.000 ARG H 71 *********************** 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 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.274 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.1624 time to fit residues: 5.7935 Evaluate side-chains 28 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.152370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134568 restraints weight = 2984.376| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.74 r_work: 0.3409 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2639 Z= 0.271 Angle : 0.546 9.474 3562 Z= 0.275 Chirality : 0.041 0.150 391 Planarity : 0.003 0.026 442 Dihedral : 4.153 14.994 343 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: 0.52 (0.50), residues: 309 helix: 3.28 (0.50), residues: 77 sheet: -0.86 (0.54), residues: 107 loop : -0.31 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 96 HIS 0.004 0.002 HIS A 663 PHE 0.010 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.002 0.000 ARG K 108 *********************** 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 35 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.313 Fit side-chains REVERT: H 12 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8401 (m) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1429 time to fit residues: 5.9138 Evaluate side-chains 32 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.152292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135522 restraints weight = 3067.458| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.64 r_work: 0.3428 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2639 Z= 0.253 Angle : 0.533 8.967 3562 Z= 0.270 Chirality : 0.040 0.150 391 Planarity : 0.003 0.025 442 Dihedral : 4.089 15.106 343 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.17 % Allowed : 12.32 % Favored : 84.51 % 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: 0.56 (0.50), residues: 309 helix: 3.40 (0.50), residues: 77 sheet: -0.82 (0.54), residues: 107 loop : -0.37 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 96 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 H 71 *********************** 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 33 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.296 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.1507 time to fit residues: 5.7775 Evaluate side-chains 31 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER 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 58 ILE 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 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.154193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137265 restraints weight = 2917.051| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.62 r_work: 0.3426 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2639 Z= 0.228 Angle : 0.523 8.516 3562 Z= 0.263 Chirality : 0.039 0.150 391 Planarity : 0.003 0.025 442 Dihedral : 3.989 14.409 343 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.82 % Allowed : 12.32 % Favored : 84.86 % 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: 0.63 (0.51), residues: 309 helix: 3.51 (0.51), residues: 77 sheet: -0.79 (0.55), residues: 107 loop : -0.35 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 96 HIS 0.004 0.002 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.011 0.002 TYR K 91 ARG 0.002 0.000 ARG H 71 *********************** 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 33 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.269 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.1424 time to fit residues: 5.5050 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 58 ILE 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 17 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 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 = 0.3683 r_free = 0.3683 target = 0.150857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133316 restraints weight = 2982.023| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.73 r_work: 0.3399 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2639 Z= 0.273 Angle : 0.551 8.871 3562 Z= 0.278 Chirality : 0.040 0.148 391 Planarity : 0.003 0.025 442 Dihedral : 4.088 14.903 343 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.46 % Allowed : 13.03 % Favored : 84.51 % 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: 0.58 (0.51), residues: 309 helix: 3.44 (0.50), residues: 77 sheet: -0.83 (0.55), residues: 107 loop : -0.37 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 96 HIS 0.005 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 108 *********************** 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 33 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.300 Fit side-chains REVERT: K 105 GLU cc_start: 0.7656 (pt0) cc_final: 0.7426 (pt0) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.1819 time to fit residues: 6.7941 Evaluate side-chains 31 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 58 ILE 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 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.0020 chunk 11 optimal weight: 0.0050 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.155037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137803 restraints weight = 2915.562| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.71 r_work: 0.3435 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2639 Z= 0.174 Angle : 0.494 6.810 3562 Z= 0.251 Chirality : 0.038 0.151 391 Planarity : 0.003 0.037 442 Dihedral : 3.800 13.464 343 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.06 % Allowed : 14.08 % Favored : 84.86 % 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: 0.74 (0.51), residues: 309 helix: 3.73 (0.52), residues: 77 sheet: -0.74 (0.56), residues: 106 loop : -0.39 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 H 71 ********************** 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 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.277 Fit side-chains REVERT: K 105 GLU cc_start: 0.7482 (pt0) cc_final: 0.7243 (pt0) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.1803 time to fit residues: 5.9184 Evaluate side-chains 28 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.154882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137455 restraints weight = 2939.104| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.73 r_work: 0.3439 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2639 Z= 0.184 Angle : 0.495 6.854 3562 Z= 0.250 Chirality : 0.038 0.148 391 Planarity : 0.003 0.027 442 Dihedral : 3.700 12.764 343 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.70 % Allowed : 14.44 % Favored : 84.86 % 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: 0.77 (0.51), residues: 309 helix: 3.88 (0.50), residues: 76 sheet: -0.76 (0.56), residues: 107 loop : -0.37 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 96 HIS 0.003 0.001 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.012 0.001 TYR K 91 ARG 0.003 0.000 ARG H 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.36 seconds wall clock time: 32 minutes 52.27 seconds (1972.27 seconds total)