Starting phenix.real_space_refine on Wed Mar 5 16:06:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdg_43149/03_2025/8vdg_43149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdg_43149/03_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_43149/03_2025/8vdg_43149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdg_43149/03_2025/8vdg_43149.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdg_43149/03_2025/8vdg_43149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdg_43149/03_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-5624/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: 3.10, per 1000 atoms: 1.20 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: 0.60 Conformation dependent library (CDL) restraints added in 310.2 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: 0.35 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: 0.68 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 803 1.34 - 1.46: 654 1.46 - 1.58: 1162 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 2639 Sorted by residual: bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.461 1.490 -0.028 9.20e-03 1.18e+04 9.53e+00 bond pdb=" N VAL K 3 " pdb=" CA VAL K 3 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.42e+00 bond pdb=" N GLU K 17 " pdb=" CA GLU K 17 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.63e+00 bond pdb=" N ASP K 18 " pdb=" CA ASP K 18 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.85e+00 bond pdb=" N LEU K 13 " pdb=" CA LEU K 13 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.67e+00 ... (remaining 2634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 3439 1.96 - 3.92: 106 3.92 - 5.88: 12 5.88 - 7.83: 4 7.83 - 9.79: 1 Bond angle restraints: 3562 Sorted by residual: angle pdb=" N ILE H 53 " pdb=" CA ILE H 53 " pdb=" C ILE H 53 " ideal model delta sigma weight residual 109.34 102.26 7.08 2.08e+00 2.31e-01 1.16e+01 angle pdb=" CB MET A 665 " pdb=" CG MET A 665 " pdb=" SD MET A 665 " ideal model delta sigma weight residual 112.70 122.49 -9.79 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ASP K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA THR K 5 " pdb=" CB THR K 5 " pdb=" OG1 THR K 5 " ideal model delta sigma weight residual 109.60 104.99 4.61 1.50e+00 4.44e-01 9.43e+00 angle pdb=" CA GLN K 6 " pdb=" C GLN K 6 " pdb=" O GLN K 6 " ideal model delta sigma weight residual 121.58 118.26 3.32 1.12e+00 7.97e-01 8.80e+00 ... (remaining 3557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 1408 15.66 - 31.32: 107 31.32 - 46.97: 41 46.97 - 62.63: 9 62.63 - 78.29: 3 Dihedral angle restraints: 1568 sinusoidal: 634 harmonic: 934 Sorted by residual: dihedral pdb=" CA MET A 665 " pdb=" C MET A 665 " pdb=" N LYS A 666 " pdb=" CA LYS A 666 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.05 -59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN K 6 " pdb=" CA GLN K 6 " pdb=" CB GLN K 6 " pdb=" CG GLN K 6 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 1565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 273 0.045 - 0.090: 83 0.090 - 0.134: 25 0.134 - 0.179: 7 0.179 - 0.224: 3 Chirality restraints: 391 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 388 not shown) Planarity restraints: 442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 67 " 0.001 2.00e-02 2.50e+03 1.97e-02 6.82e+00 pdb=" CG PHE H 67 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE H 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE H 67 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 67 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 96 " -0.010 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP K 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP K 96 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP K 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 96 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 96 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 96 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 96 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO H 97 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " -0.023 5.00e-02 4.00e+02 ... (remaining 439 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 645 2.80 - 3.32: 2132 3.32 - 3.85: 4378 3.85 - 4.37: 4955 4.37 - 4.90: 9045 Nonbonded interactions: 21155 Sorted by model distance: nonbonded pdb=" OE1 GLU H 33 " pdb=" OH TYR H 50 " model vdw 2.274 3.040 nonbonded pdb=" O TYR K 49 " pdb=" OH TYR K 91 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 680 " pdb=" OH TYR A 707 " model vdw 2.310 3.040 nonbonded pdb=" O ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.332 3.040 nonbonded pdb=" NH1 ARG K 54 " pdb=" O ILE K 58 " model vdw 2.379 3.120 ... (remaining 21150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.490 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- 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 : 0.285 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: 0.2311 time to fit residues: 9.3208 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 : 0.293 ------------------------------------------------------------------------------- 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 = 44)----------------| | 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: 0.3469 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.285 Fit side-chains revert: symmetry clash REVERT: A 658 GLU cc_start: 0.8420 (tt0) cc_final: 0.7156 (mp0) REVERT: A 665 MET cc_start: 0.8036 (mmp) cc_final: 0.7712 (mmp) REVERT: H 85 GLU cc_start: 0.7698 (pm20) cc_final: 0.7494 (pm20) REVERT: K 52 SER cc_start: 0.8468 (p) cc_final: 0.8252 (m) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2428 time to fit residues: 8.9797 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 : 0.292 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.167463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148662 restraints weight = 2979.655| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.78 r_work: 0.3516 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2639 Z= 0.305 Angle : 0.599 10.934 3562 Z= 0.304 Chirality : 0.042 0.153 391 Planarity : 0.004 0.038 442 Dihedral : 4.443 13.899 343 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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: -0.01 (0.48), residues: 309 helix: 2.50 (0.51), residues: 77 sheet: -1.23 (0.50), residues: 107 loop : -0.32 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.005 0.003 HIS A 663 PHE 0.012 0.002 PHE A 662 TYR 0.018 0.002 TYR K 91 ARG 0.003 0.001 ARG K 108 *********************** 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 : 0.298 Fit side-chains REVERT: A 658 GLU cc_start: 0.8369 (tt0) cc_final: 0.8161 (tt0) REVERT: A 665 MET cc_start: 0.8075 (mmp) cc_final: 0.7731 (mmp) REVERT: K 52 SER cc_start: 0.8546 (p) cc_final: 0.8339 (m) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1962 time to fit residues: 6.5866 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 : 0.248 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.154031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136024 restraints weight = 2954.213| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.74 r_work: 0.3423 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 2639 Z= 0.259 Angle : 0.540 9.828 3562 Z= 0.273 Chirality : 0.041 0.146 391 Planarity : 0.003 0.028 442 Dihedral : 4.236 14.485 343 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.41 % Allowed : 11.62 % 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: 0.25 (0.48), residues: 309 helix: 2.94 (0.51), residues: 77 sheet: -1.05 (0.51), residues: 107 loop : -0.35 (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 0.009 0.001 PHE H 67 TYR 0.013 0.002 TYR K 91 ARG 0.002 0.000 ARG H 100B *********************** 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 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.271 Fit side-chains REVERT: A 665 MET cc_start: 0.7990 (mmp) cc_final: 0.7527 (mmp) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.1604 time to fit residues: 5.5793 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 : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.154837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137232 restraints weight = 2939.255| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.68 r_work: 0.3425 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3145 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= 0.241 Angle : 0.524 9.377 3562 Z= 0.265 Chirality : 0.040 0.148 391 Planarity : 0.003 0.026 442 Dihedral : 4.121 14.465 343 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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: 0.48 (0.49), residues: 309 helix: 3.19 (0.51), residues: 77 sheet: -0.89 (0.53), residues: 107 loop : -0.29 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.009 0.001 PHE A 662 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 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.267 Fit side-chains REVERT: H 12 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (m) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.1655 time to fit residues: 5.7172 Evaluate side-chains 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 56 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: 0.4980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.155640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137573 restraints weight = 2952.991| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.77 r_work: 0.3426 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2639 Z= 0.183 Angle : 0.483 8.285 3562 Z= 0.245 Chirality : 0.038 0.147 391 Planarity : 0.003 0.026 442 Dihedral : 3.873 13.314 343 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.46 % Allowed : 11.62 % 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: 0.77 (0.50), residues: 309 helix: 3.52 (0.51), residues: 77 sheet: -0.70 (0.55), residues: 107 loop : -0.21 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 79 HIS 0.002 0.001 HIS A 663 PHE 0.007 0.001 PHE A 662 TYR 0.012 0.001 TYR K 91 ARG 0.002 0.000 ARG H 71 *********************** 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 36 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.291 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.1472 time to fit residues: 6.3086 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.0030 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.153316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135631 restraints weight = 3041.615| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.77 r_work: 0.3433 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2639 Z= 0.193 Angle : 0.494 7.811 3562 Z= 0.249 Chirality : 0.038 0.148 391 Planarity : 0.003 0.026 442 Dihedral : 3.822 13.138 343 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.76 % Allowed : 13.73 % 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: 0.85 (0.51), residues: 309 helix: 3.62 (0.51), residues: 77 sheet: -0.67 (0.56), residues: 107 loop : -0.17 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 96 HIS 0.003 0.002 HIS A 663 PHE 0.007 0.001 PHE A 662 TYR 0.011 0.001 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 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.277 Fit side-chains REVERT: K 105 GLU cc_start: 0.7605 (pt0) cc_final: 0.7385 (pt0) outliers start: 5 outliers final: 5 residues processed: 27 average time/residue: 0.1696 time to fit residues: 5.6830 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=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: 0.9980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.0000 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.155235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137700 restraints weight = 2914.470| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.72 r_work: 0.3449 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2639 Z= 0.185 Angle : 0.481 7.612 3562 Z= 0.244 Chirality : 0.038 0.148 391 Planarity : 0.003 0.025 442 Dihedral : 3.720 12.841 343 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.82 % Allowed : 12.68 % 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: 0.92 (0.52), residues: 309 helix: 3.71 (0.51), residues: 77 sheet: -0.66 (0.57), residues: 107 loop : -0.12 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.003 0.002 HIS A 663 PHE 0.007 0.001 PHE A 662 TYR 0.011 0.001 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 32 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.294 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.1603 time to fit residues: 5.9584 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.153408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136469 restraints weight = 2971.511| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.64 r_work: 0.3424 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2639 Z= 0.235 Angle : 0.520 7.883 3562 Z= 0.262 Chirality : 0.040 0.146 391 Planarity : 0.003 0.024 442 Dihedral : 3.840 13.235 343 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.11 % Allowed : 13.73 % 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: 0.85 (0.51), residues: 309 helix: 3.61 (0.51), residues: 77 sheet: -0.70 (0.56), residues: 107 loop : -0.12 (0.58), 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 0.009 0.001 PHE A 662 TYR 0.012 0.002 TYR K 91 ARG 0.001 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 32 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.270 Fit side-chains REVERT: H 53 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7038 (mm) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.1826 time to fit residues: 6.5840 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 : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE 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 16 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.152502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135429 restraints weight = 2936.926| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.70 r_work: 0.3428 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2639 Z= 0.205 Angle : 0.511 7.266 3562 Z= 0.257 Chirality : 0.039 0.147 391 Planarity : 0.003 0.036 442 Dihedral : 3.779 13.640 343 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.76 % Allowed : 14.08 % 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: 0.83 (0.51), residues: 309 helix: 3.72 (0.51), residues: 77 sheet: -0.73 (0.56), residues: 107 loop : -0.21 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 PHE 0.008 0.001 PHE A 662 TYR 0.012 0.001 TYR K 91 ARG 0.003 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 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.272 Fit side-chains REVERT: H 53 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6868 (mm) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1542 time to fit residues: 5.3761 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE 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: 0.5980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.3688 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.158641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140877 restraints weight = 2921.041| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.74 r_work: 0.3464 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2639 Z= 0.163 Angle : 0.475 6.621 3562 Z= 0.240 Chirality : 0.038 0.145 391 Planarity : 0.003 0.025 442 Dihedral : 3.547 12.577 343 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.11 % Allowed : 14.08 % Favored : 83.80 % 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: 0.94 (0.52), residues: 309 helix: 4.00 (0.50), residues: 76 sheet: -0.68 (0.57), residues: 107 loop : -0.24 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 79 HIS 0.002 0.001 HIS A 663 PHE 0.007 0.001 PHE H 67 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: 1887.76 seconds wall clock time: 33 minutes 8.78 seconds (1988.78 seconds total)