Starting phenix.real_space_refine on Sat Apr 26 16:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdg_43149/04_2025/8vdg_43149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdg_43149/04_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_43149/04_2025/8vdg_43149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdg_43149/04_2025/8vdg_43149.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdg_43149/04_2025/8vdg_43149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdg_43149/04_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-5669/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: 2.40, per 1000 atoms: 0.93 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: 0.53 Conformation dependent library (CDL) restraints added in 269.6 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: 0.31 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: 0.61 Time building geometry restraints manager: 0.65 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.790 Find NCS groups from input model: 0.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- 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 2642 Z= 0.311 Angle : 0.821 9.793 3568 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 Details of bonding type rmsd hydrogen bonds : bond 0.18643 ( 106) hydrogen bonds : angle 8.00241 ( 291) SS BOND : bond 0.00295 ( 3) SS BOND : angle 1.08332 ( 6) covalent geometry : bond 0.00564 ( 2639) covalent geometry : angle 0.82083 ( 3562) *********************** 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 : 0.291 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: 0.2338 time to fit residues: 9.4456 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 : 0.297 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.176050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157362 restraints weight = 2933.580| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.81 r_work: 0.3602 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2642 Z= 0.171 Angle : 0.595 12.493 3568 Z= 0.301 Chirality : 0.041 0.146 391 Planarity : 0.004 0.029 442 Dihedral : 4.169 14.007 343 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.35 % Allowed : 7.39 % Favored : 92.25 % 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: -0.21 (0.48), residues: 309 helix: 1.79 (0.51), residues: 77 sheet: -1.18 (0.52), residues: 102 loop : -0.27 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.013 0.002 PHE A 662 TYR 0.015 0.002 TYR K 49 ARG 0.005 0.001 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 106) hydrogen bonds : angle 5.18498 ( 291) SS BOND : bond 0.00592 ( 3) SS BOND : angle 0.84525 ( 6) covalent geometry : bond 0.00404 ( 2639) covalent geometry : angle 0.59496 ( 3562) *********************** 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: 1 poor density : 31 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 658 GLU cc_start: 0.8408 (tt0) cc_final: 0.7209 (mp0) REVERT: A 665 MET cc_start: 0.8084 (mmp) cc_final: 0.7685 (mmp) REVERT: H 85 GLU cc_start: 0.7740 (pm20) cc_final: 0.7526 (pm20) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.2436 time to fit residues: 8.9926 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.0060 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.171637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152954 restraints weight = 2956.277| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.79 r_work: 0.3560 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2642 Z= 0.153 Angle : 0.538 9.202 3568 Z= 0.272 Chirality : 0.040 0.149 391 Planarity : 0.004 0.031 442 Dihedral : 4.103 12.928 343 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.06 % Allowed : 10.21 % Favored : 88.73 % 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: 0.30 (0.49), residues: 309 helix: 2.74 (0.51), residues: 77 sheet: -1.05 (0.52), residues: 107 loop : -0.11 (0.57), 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 0.017 0.002 TYR K 91 ARG 0.003 0.001 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 106) hydrogen bonds : angle 4.91043 ( 291) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.72971 ( 6) covalent geometry : bond 0.00367 ( 2639) covalent geometry : angle 0.53740 ( 3562) *********************** 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 31 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.309 Fit side-chains REVERT: A 665 MET cc_start: 0.8049 (mmp) cc_final: 0.7572 (mmp) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.1626 time to fit residues: 5.8535 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.0370 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.153071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135315 restraints weight = 2957.214| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.75 r_work: 0.3434 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 2642 Z= 0.158 Angle : 0.526 9.247 3568 Z= 0.265 Chirality : 0.040 0.141 391 Planarity : 0.003 0.028 442 Dihedral : 4.063 13.752 343 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 0.44 (0.49), residues: 309 helix: 3.13 (0.50), residues: 77 sheet: -0.94 (0.52), residues: 107 loop : -0.27 (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 A 662 TYR 0.013 0.002 TYR K 91 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 106) hydrogen bonds : angle 4.73868 ( 291) SS BOND : bond 0.00237 ( 3) SS BOND : angle 0.65351 ( 6) covalent geometry : bond 0.00395 ( 2639) covalent geometry : angle 0.52610 ( 3562) *********************** 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 31 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.296 Fit side-chains REVERT: A 665 MET cc_start: 0.7979 (mmp) cc_final: 0.7533 (mmp) REVERT: H 85 GLU cc_start: 0.7793 (pm20) cc_final: 0.7583 (pm20) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1650 time to fit residues: 5.7472 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 : 0.294 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4666 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.156747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138914 restraints weight = 2925.649| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.74 r_work: 0.3445 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2642 Z= 0.122 Angle : 0.480 8.098 3568 Z= 0.243 Chirality : 0.038 0.144 391 Planarity : 0.003 0.028 442 Dihedral : 3.821 12.897 343 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.41 % Allowed : 12.68 % Favored : 85.92 % 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: 0.70 (0.50), residues: 309 helix: 3.49 (0.51), residues: 77 sheet: -0.77 (0.54), residues: 107 loop : -0.24 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 79 HIS 0.003 0.001 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.013 0.002 TYR K 91 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 106) hydrogen bonds : angle 4.50432 ( 291) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.44871 ( 6) covalent geometry : bond 0.00294 ( 2639) covalent geometry : angle 0.47968 ( 3562) *********************** 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 to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.299 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.1695 time to fit residues: 5.6498 Evaluate side-chains 26 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.156839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138617 restraints weight = 2949.246| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.78 r_work: 0.3438 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2642 Z= 0.140 Angle : 0.494 8.127 3568 Z= 0.250 Chirality : 0.039 0.144 391 Planarity : 0.003 0.027 442 Dihedral : 3.851 13.413 343 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 12.68 % 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: 0.74 (0.50), residues: 309 helix: 3.53 (0.50), residues: 77 sheet: -0.70 (0.54), residues: 107 loop : -0.26 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 96 HIS 0.003 0.001 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 106) hydrogen bonds : angle 4.48361 ( 291) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.53040 ( 6) covalent geometry : bond 0.00340 ( 2639) covalent geometry : angle 0.49354 ( 3562) *********************** 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 32 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.299 Fit side-chains REVERT: H 12 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (m) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.1486 time to fit residues: 5.9704 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 : 0.262 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 26 optimal weight: 0.0070 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.157175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139614 restraints weight = 3021.283| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.71 r_work: 0.3432 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2642 Z= 0.130 Angle : 0.482 7.753 3568 Z= 0.245 Chirality : 0.039 0.145 391 Planarity : 0.003 0.026 442 Dihedral : 3.759 13.084 343 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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: 0.87 (0.51), residues: 309 helix: 3.64 (0.51), residues: 77 sheet: -0.66 (0.55), residues: 107 loop : -0.15 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 96 HIS 0.003 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 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 106) hydrogen bonds : angle 4.39675 ( 291) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.45736 ( 6) covalent geometry : bond 0.00316 ( 2639) covalent geometry : angle 0.48158 ( 3562) *********************** 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 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.253 Fit side-chains REVERT: H 53 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7188 (mm) REVERT: K 105 GLU cc_start: 0.7982 (pt0) cc_final: 0.7778 (pt0) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.1579 time to fit residues: 5.6314 Evaluate side-chains 28 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 ILE 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 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.153843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136404 restraints weight = 2923.199| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.72 r_work: 0.3428 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2642 Z= 0.144 Angle : 0.490 7.946 3568 Z= 0.250 Chirality : 0.039 0.145 391 Planarity : 0.003 0.026 442 Dihedral : 3.808 13.368 343 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.41 % Allowed : 13.73 % 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: 0.83 (0.51), residues: 309 helix: 3.62 (0.51), residues: 77 sheet: -0.71 (0.55), residues: 107 loop : -0.16 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 106) hydrogen bonds : angle 4.41695 ( 291) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.54526 ( 6) covalent geometry : bond 0.00349 ( 2639) covalent geometry : angle 0.48989 ( 3562) *********************** 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 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.276 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.2022 time to fit residues: 6.7783 Evaluate side-chains 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.151481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135193 restraints weight = 2970.985| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.60 r_work: 0.3415 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2642 Z= 0.155 Angle : 0.527 7.968 3568 Z= 0.266 Chirality : 0.040 0.180 391 Planarity : 0.003 0.036 442 Dihedral : 3.827 13.373 343 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.41 % Allowed : 13.73 % 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: 0.79 (0.50), residues: 309 helix: 3.62 (0.51), residues: 77 sheet: -0.72 (0.55), residues: 107 loop : -0.23 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 49 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 106) hydrogen bonds : angle 4.44463 ( 291) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.55448 ( 6) covalent geometry : bond 0.00377 ( 2639) covalent geometry : angle 0.52665 ( 3562) *********************** 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 28 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.303 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.1766 time to fit residues: 5.8818 Evaluate side-chains 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.155344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138307 restraints weight = 2916.319| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.68 r_work: 0.3438 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2642 Z= 0.142 Angle : 0.524 7.647 3568 Z= 0.263 Chirality : 0.040 0.175 391 Planarity : 0.003 0.026 442 Dihedral : 3.773 13.141 343 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.76 % Allowed : 13.38 % 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: 0.82 (0.51), residues: 309 helix: 3.67 (0.51), residues: 77 sheet: -0.70 (0.56), residues: 107 loop : -0.22 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.004 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 106) hydrogen bonds : angle 4.41222 ( 291) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.50164 ( 6) covalent geometry : bond 0.00346 ( 2639) covalent geometry : angle 0.52383 ( 3562) ********************** 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 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.260 Fit side-chains REVERT: K 105 GLU cc_start: 0.7522 (pt0) cc_final: 0.7316 (pt0) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1622 time to fit residues: 5.5908 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 : 0.277 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.157864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140521 restraints weight = 2919.243| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.71 r_work: 0.3466 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2642 Z= 0.113 Angle : 0.491 6.720 3568 Z= 0.248 Chirality : 0.038 0.170 391 Planarity : 0.003 0.026 442 Dihedral : 3.592 12.524 343 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.41 % Allowed : 14.44 % Favored : 84.15 % 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: 3.93 (0.50), residues: 76 sheet: -0.69 (0.56), residues: 107 loop : -0.31 (0.55), residues: 126 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 H 67 TYR 0.011 0.001 TYR K 91 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.02394 ( 106) hydrogen bonds : angle 4.23741 ( 291) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.37544 ( 6) covalent geometry : bond 0.00271 ( 2639) covalent geometry : angle 0.49109 ( 3562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.13 seconds wall clock time: 34 minutes 36.21 seconds (2076.21 seconds total)