Starting phenix.real_space_refine on Mon Feb 10 20:09:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf3_37197/02_2025/8kf3_37197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf3_37197/02_2025/8kf3_37197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kf3_37197/02_2025/8kf3_37197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf3_37197/02_2025/8kf3_37197.map" model { file = "/net/cci-nas-00/data/ceres_data/8kf3_37197/02_2025/8kf3_37197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf3_37197/02_2025/8kf3_37197.cif" } resolution = 3.5 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= 0.001 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 9 5.16 5 C 1419 2.51 5 N 369 2.21 5 O 378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 2.39, per 1000 atoms: 1.10 Number of scatterers: 2175 At special positions: 0 Unit cell: (63.91, 95.45, 39.84, 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 9 16.00 O 378 8.00 N 369 7.00 C 1419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.46 Conformation dependent library (CDL) restraints added in 304.9 milliseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AA3, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.609A pdb=" N ILE D 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET E 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE E 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N MET F 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 18 removed outlier: 9.112A pdb=" N GLU H 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N HIS G 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS H 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LYS G 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN H 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL G 18 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU H 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL I 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 30 through 35 removed outlier: 6.250A pdb=" N ILE H 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU G 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY H 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU I 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY G 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 15 removed outlier: 6.377A pdb=" N TYR B 10 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS A 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 12 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A 15 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS B 14 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS C 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN C 15 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N HIS A 14 " --> pdb=" O GLN C 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.173A pdb=" N ILE B 31 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 41 20 hydrogen bonds defined for protein. 60 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: 0.49 Time building geometry restraints manager: 0.54 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: 705 1.34 - 1.45: 294 1.45 - 1.57: 1191 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 2208 Sorted by residual: bond pdb=" CB LYS C 16 " pdb=" CG LYS C 16 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" N GLY G 29 " pdb=" CA GLY G 29 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.23e+00 bond pdb=" CB LYS A 16 " pdb=" CG LYS A 16 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CG GLN G 15 " pdb=" CD GLN G 15 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB LYS B 16 " pdb=" CG LYS B 16 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 2203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 2668 1.34 - 2.68: 243 2.68 - 4.02: 38 4.02 - 5.36: 13 5.36 - 6.70: 2 Bond angle restraints: 2964 Sorted by residual: angle pdb=" N ASP G 23 " pdb=" CA ASP G 23 " pdb=" CB ASP G 23 " ideal model delta sigma weight residual 114.17 109.99 4.18 1.14e+00 7.69e-01 1.34e+01 angle pdb=" C GLU C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N VAL E 36 " pdb=" CA VAL E 36 " pdb=" C VAL E 36 " ideal model delta sigma weight residual 111.62 108.89 2.73 7.90e-01 1.60e+00 1.20e+01 angle pdb=" N ASP H 23 " pdb=" CA ASP H 23 " pdb=" CB ASP H 23 " ideal model delta sigma weight residual 114.17 110.44 3.73 1.14e+00 7.69e-01 1.07e+01 angle pdb=" C GLU A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 ... (remaining 2959 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.76: 1015 11.76 - 23.52: 139 23.52 - 35.28: 51 35.28 - 47.03: 21 47.03 - 58.79: 4 Dihedral angle restraints: 1230 sinusoidal: 444 harmonic: 786 Sorted by residual: dihedral pdb=" CA ASP C 23 " pdb=" C ASP C 23 " pdb=" N VAL C 24 " pdb=" CA VAL C 24 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 23 " pdb=" C ASP A 23 " pdb=" N VAL A 24 " pdb=" CA VAL A 24 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP B 23 " pdb=" C ASP B 23 " pdb=" N VAL B 24 " pdb=" CA VAL B 24 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 124 0.027 - 0.053: 86 0.053 - 0.080: 48 0.080 - 0.107: 47 0.107 - 0.133: 40 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA HIS H 14 " pdb=" N HIS H 14 " pdb=" C HIS H 14 " pdb=" CB HIS H 14 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL I 12 " pdb=" N VAL I 12 " pdb=" C VAL I 12 " pdb=" CB VAL I 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 342 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 23 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ASP H 23 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP H 23 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL H 24 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 22 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C GLU I 22 " 0.018 2.00e-02 2.50e+03 pdb=" O GLU I 22 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP I 23 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 23 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.77e-01 pdb=" C ASP G 23 " 0.015 2.00e-02 2.50e+03 pdb=" O ASP G 23 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL G 24 " -0.005 2.00e-02 2.50e+03 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 722 2.88 - 3.39: 1695 3.39 - 3.89: 3635 3.89 - 4.40: 3687 4.40 - 4.90: 7218 Nonbonded interactions: 16957 Sorted by model distance: nonbonded pdb=" O VAL D 12 " pdb=" N VAL E 12 " model vdw 2.379 3.120 nonbonded pdb=" OE2 GLU H 22 " pdb=" NZ LYS G 16 " model vdw 2.573 3.120 nonbonded pdb=" ND2 ASN C 27 " pdb=" O GLY C 29 " model vdw 2.588 3.120 nonbonded pdb=" ND2 ASN A 27 " pdb=" O GLY A 29 " model vdw 2.590 3.120 nonbonded pdb=" O VAL E 12 " pdb=" N VAL F 12 " model vdw 2.604 3.120 ... (remaining 16952 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 42) selection = (chain 'B' and resid 12 through 42) selection = (chain 'C' and resid 12 through 42) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 12 through 42) selection = (chain 'H' and resid 12 through 42) selection = (chain 'I' and resid 12 through 42) } 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 group one per residue 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: 1.020 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: 0.010 Set scattering table: 0.020 Process input model: 10.940 Find NCS groups from input model: 0.110 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.008 0.034 2208 Z= 0.560 Angle : 0.862 6.696 2964 Z= 0.502 Chirality : 0.063 0.133 345 Planarity : 0.003 0.011 372 Dihedral : 13.984 58.791 738 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.58 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 14 PHE 0.009 0.002 PHE C 20 TYR 0.006 0.002 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.551 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1591 time to fit residues: 5.6758 Evaluate side-chains 22 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 27 ASN H 13 HIS E 27 ASN G 13 HIS F 15 GLN F 27 ASN I 13 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096629 restraints weight = 2297.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097930 restraints weight = 1865.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098402 restraints weight = 1653.546| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2208 Z= 0.160 Angle : 0.558 5.573 2964 Z= 0.301 Chirality : 0.058 0.146 345 Planarity : 0.002 0.014 372 Dihedral : 4.459 12.967 294 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.83 % Allowed : 7.31 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.94 (0.44), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 13 PHE 0.004 0.001 PHE E 19 TYR 0.004 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.227 Fit side-chains REVERT: D 15 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: G 28 LYS cc_start: 0.8429 (mttt) cc_final: 0.7945 (mtpp) outliers start: 4 outliers final: 0 residues processed: 29 average time/residue: 0.1348 time to fit residues: 4.7935 Evaluate side-chains 23 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 0.0020 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.5594 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.128716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104171 restraints weight = 2309.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104213 restraints weight = 2271.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104213 restraints weight = 2252.733| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2208 Z= 0.401 Angle : 0.686 7.131 2964 Z= 0.371 Chirality : 0.060 0.132 345 Planarity : 0.003 0.016 372 Dihedral : 4.655 12.862 294 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.83 % Allowed : 12.79 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.83 (0.45), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 14 PHE 0.007 0.002 PHE E 20 TYR 0.006 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.279 Fit side-chains REVERT: E 34 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8334 (tt) REVERT: F 34 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (tt) REVERT: F 35 MET cc_start: 0.8258 (tpt) cc_final: 0.7702 (tpt) outliers start: 4 outliers final: 0 residues processed: 25 average time/residue: 0.1520 time to fit residues: 4.6825 Evaluate side-chains 23 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105900 restraints weight = 2359.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106110 restraints weight = 2246.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106155 restraints weight = 2187.924| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2208 Z= 0.294 Angle : 0.607 6.791 2964 Z= 0.329 Chirality : 0.059 0.129 345 Planarity : 0.002 0.014 372 Dihedral : 4.443 11.821 294 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.28 % Allowed : 13.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.66 (0.46), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 14 PHE 0.006 0.001 PHE E 20 TYR 0.005 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.237 Fit side-chains REVERT: D 15 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: E 34 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8314 (tt) REVERT: F 34 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8342 (tt) outliers start: 5 outliers final: 1 residues processed: 26 average time/residue: 0.1459 time to fit residues: 4.7300 Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102804 restraints weight = 2305.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103708 restraints weight = 2006.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103708 restraints weight = 1824.983| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2208 Z= 0.289 Angle : 0.607 5.871 2964 Z= 0.328 Chirality : 0.059 0.131 345 Planarity : 0.002 0.013 372 Dihedral : 4.328 12.090 294 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.28 % Allowed : 14.16 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.55 (0.47), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 14 PHE 0.006 0.001 PHE F 20 TYR 0.006 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.237 Fit side-chains REVERT: E 34 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8280 (tt) REVERT: F 34 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8349 (tt) outliers start: 5 outliers final: 1 residues processed: 26 average time/residue: 0.1342 time to fit residues: 4.3308 Evaluate side-chains 24 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.127479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101686 restraints weight = 2322.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101688 restraints weight = 2187.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101688 restraints weight = 2186.669| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2208 Z= 0.441 Angle : 0.693 5.656 2964 Z= 0.377 Chirality : 0.061 0.133 345 Planarity : 0.003 0.015 372 Dihedral : 4.592 13.146 294 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.28 % Allowed : 15.53 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.48), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 14 PHE 0.008 0.002 PHE F 20 TYR 0.008 0.002 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.238 Fit side-chains REVERT: D 34 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8365 (tt) REVERT: E 34 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8289 (tt) REVERT: F 34 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8364 (tt) outliers start: 5 outliers final: 0 residues processed: 27 average time/residue: 0.1414 time to fit residues: 4.7200 Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.127648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097998 restraints weight = 2294.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099430 restraints weight = 1874.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100475 restraints weight = 1652.365| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2208 Z= 0.142 Angle : 0.515 5.891 2964 Z= 0.277 Chirality : 0.058 0.142 345 Planarity : 0.002 0.012 372 Dihedral : 3.901 11.405 294 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.91 % Allowed : 16.44 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.37 (0.48), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 13 PHE 0.005 0.001 PHE D 19 TYR 0.004 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.246 Fit side-chains REVERT: D 34 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8290 (tt) REVERT: E 34 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8227 (tt) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.1485 time to fit residues: 5.0865 Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.0470 chunk 25 optimal weight: 0.0570 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.122252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.092364 restraints weight = 2388.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.093277 restraints weight = 1988.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094267 restraints weight = 1811.651| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2208 Z= 0.296 Angle : 0.599 5.813 2964 Z= 0.328 Chirality : 0.059 0.131 345 Planarity : 0.002 0.013 372 Dihedral : 4.142 12.381 294 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.37 % Allowed : 17.35 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.40 (0.48), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 14 PHE 0.006 0.001 PHE F 20 TYR 0.012 0.002 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.184 Fit side-chains REVERT: D 34 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8355 (tt) REVERT: E 34 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8253 (tt) REVERT: F 34 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8343 (tt) outliers start: 3 outliers final: 0 residues processed: 28 average time/residue: 0.1251 time to fit residues: 4.2944 Evaluate side-chains 27 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106853 restraints weight = 2302.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108020 restraints weight = 1911.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108849 restraints weight = 1686.879| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2208 Z= 0.177 Angle : 0.526 5.567 2964 Z= 0.285 Chirality : 0.058 0.129 345 Planarity : 0.002 0.012 372 Dihedral : 3.911 11.296 294 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.37 % Allowed : 17.81 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.32 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 14 PHE 0.005 0.001 PHE F 20 TYR 0.009 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.254 Fit side-chains REVERT: D 34 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8379 (tt) REVERT: E 34 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8244 (tt) REVERT: F 34 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8342 (tt) outliers start: 3 outliers final: 0 residues processed: 28 average time/residue: 0.1319 time to fit residues: 4.5515 Evaluate side-chains 27 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.128249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.100810 restraints weight = 2316.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101508 restraints weight = 2060.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101847 restraints weight = 1902.551| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2208 Z= 0.401 Angle : 0.661 5.592 2964 Z= 0.362 Chirality : 0.060 0.134 345 Planarity : 0.002 0.016 372 Dihedral : 4.352 13.072 294 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.37 % Allowed : 17.35 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.40 (0.48), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 14 PHE 0.008 0.002 PHE F 20 TYR 0.015 0.002 TYR G 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.227 Fit side-chains REVERT: D 34 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8369 (tt) REVERT: E 34 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8278 (tt) REVERT: F 34 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (tt) outliers start: 3 outliers final: 0 residues processed: 28 average time/residue: 0.1347 time to fit residues: 4.6882 Evaluate side-chains 26 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.122529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092119 restraints weight = 2267.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.093399 restraints weight = 1856.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094307 restraints weight = 1633.957| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2208 Z= 0.203 Angle : 0.539 5.593 2964 Z= 0.293 Chirality : 0.058 0.130 345 Planarity : 0.002 0.014 372 Dihedral : 3.973 11.460 294 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.37 % Allowed : 16.89 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.30 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 13 PHE 0.005 0.001 PHE F 20 TYR 0.009 0.001 TYR G 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.98 seconds wall clock time: 21 minutes 8.37 seconds (1268.37 seconds total)