Starting phenix.real_space_refine on Fri Aug 22 13:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5u_37304/08_2025/8w5u_37304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5u_37304/08_2025/8w5u_37304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5u_37304/08_2025/8w5u_37304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5u_37304/08_2025/8w5u_37304.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5u_37304/08_2025/8w5u_37304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5u_37304/08_2025/8w5u_37304.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 sd= 0.087 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 11 5.16 5 C 2261 2.51 5 N 604 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3588 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 938 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 1 Chain: "c" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 959 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.31 Number of scatterers: 3588 At special positions: 0 Unit cell: (96.36, 66, 79.2, 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 11 16.00 O 712 8.00 N 604 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " 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: 0.31 Conformation dependent library (CDL) restraints added in 137.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 5 sheets defined 11.6% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.613A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'c' and resid 41 through 45 removed outlier: 4.066A pdb=" N GLU c 45 " --> pdb=" O PRO c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 102 through 116 Processing helix chain 'c' and resid 118 through 126 removed outlier: 4.099A pdb=" N ASP c 123 " --> pdb=" O PRO c 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 63 removed outlier: 6.407A pdb=" N TRP L 44 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR L 58 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU L 42 " --> pdb=" O TYR L 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 9 removed outlier: 3.724A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP H 76 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR H 83 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR H 74 " --> pdb=" O TYR H 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 72 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 63 removed outlier: 4.025A pdb=" N ILE H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR H 53 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 37 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER H 110 " --> pdb=" O THR H 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 11 removed outlier: 4.137A pdb=" N PHE C 10 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN C 17 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG c 86 " --> pdb=" O THR c 72 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL c 32 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL c 26 " --> pdb=" O VAL c 32 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N SER c 34 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN c 17 " --> pdb=" O PHE c 10 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE c 10 " --> pdb=" O GLN c 17 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 336 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: 0.48 Time building geometry restraints manager: 0.39 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: 1164 1.34 - 1.46: 812 1.46 - 1.57: 1670 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 3660 Sorted by residual: bond pdb=" CA PHE H 54 " pdb=" CB PHE H 54 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.70e-02 3.46e+03 1.21e+00 bond pdb=" C SER L 10 " pdb=" N PRO L 11 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.33e-02 5.65e+03 9.98e-01 bond pdb=" CG LEU L 42 " pdb=" CD1 LEU L 42 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.25e-01 bond pdb=" CG LEU C 116 " pdb=" CD2 LEU C 116 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.39e-01 bond pdb=" CB VAL C 52 " pdb=" CG2 VAL C 52 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 7.99e-01 ... (remaining 3655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 4770 1.58 - 3.15: 180 3.15 - 4.73: 24 4.73 - 6.30: 4 6.30 - 7.88: 1 Bond angle restraints: 4979 Sorted by residual: angle pdb=" CA VAL C 41 " pdb=" C VAL C 41 " pdb=" N PRO C 42 " ideal model delta sigma weight residual 116.57 119.75 -3.18 9.80e-01 1.04e+00 1.05e+01 angle pdb=" C VAL C 41 " pdb=" CA VAL C 41 " pdb=" CB VAL C 41 " ideal model delta sigma weight residual 109.33 112.23 -2.90 9.80e-01 1.04e+00 8.73e+00 angle pdb=" C TRP L 59 " pdb=" N ALA L 60 " pdb=" CA ALA L 60 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.22e+00 angle pdb=" CA LEU H 48 " pdb=" CB LEU H 48 " pdb=" CG LEU H 48 " ideal model delta sigma weight residual 116.30 124.18 -7.88 3.50e+00 8.16e-02 5.07e+00 angle pdb=" C THR c 18 " pdb=" N LEU c 19 " pdb=" CA LEU c 19 " ideal model delta sigma weight residual 122.73 119.32 3.41 1.62e+00 3.81e-01 4.42e+00 ... (remaining 4974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 1937 16.29 - 32.57: 200 32.57 - 48.85: 35 48.85 - 65.14: 7 65.14 - 81.42: 5 Dihedral angle restraints: 2184 sinusoidal: 821 harmonic: 1363 Sorted by residual: dihedral pdb=" CA SER H 10 " pdb=" C SER H 10 " pdb=" N GLY H 11 " pdb=" CA GLY H 11 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLN L 98 " pdb=" C GLN L 98 " pdb=" N GLN L 99 " pdb=" CA GLN L 99 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA PRO L 11 " pdb=" C PRO L 11 " pdb=" N SER L 12 " pdb=" CA SER L 12 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 2181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 338 0.031 - 0.061: 137 0.061 - 0.092: 60 0.092 - 0.122: 34 0.122 - 0.153: 5 Chirality restraints: 574 Sorted by residual: chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE L 57 " pdb=" N ILE L 57 " pdb=" C ILE L 57 " pdb=" CB ILE L 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL c 48 " pdb=" N VAL c 48 " pdb=" C VAL c 48 " pdb=" CB VAL c 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 571 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 39 " -0.010 2.00e-02 2.50e+03 9.51e-03 2.26e+00 pdb=" CG TRP H 39 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP H 39 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 39 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 39 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 39 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 129 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO C 130 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 86 " -0.105 9.50e-02 1.11e+02 4.74e-02 1.64e+00 pdb=" NE ARG C 86 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 86 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 86 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 86 " -0.001 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 145 2.70 - 3.25: 3625 3.25 - 3.80: 5487 3.80 - 4.35: 6422 4.35 - 4.90: 11057 Nonbonded interactions: 26736 Sorted by model distance: nonbonded pdb=" O LEU c 8 " pdb=" OG1 THR c 18 " model vdw 2.155 3.040 nonbonded pdb=" OG SER L 76 " pdb=" O ASP L 79 " model vdw 2.174 3.040 nonbonded pdb=" OG SER c 79 " pdb=" OD1 ASP c 81 " model vdw 2.220 3.040 nonbonded pdb=" O SER L 85 " pdb=" NZ LYS L 88 " model vdw 2.229 3.120 nonbonded pdb=" ND2 ASN c 27 " pdb=" OD1 ASN c 30 " model vdw 2.242 3.120 ... (remaining 26731 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 'C' selection = (chain 'c' and (resid 1 through 55 or resid 61 through 131)) } 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.005 0.034 3661 Z= 0.235 Angle : 0.696 7.879 4981 Z= 0.370 Chirality : 0.045 0.153 574 Planarity : 0.004 0.047 641 Dihedral : 13.917 81.424 1305 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.38), residues: 461 helix: -0.25 (0.74), residues: 45 sheet: -0.80 (0.39), residues: 179 loop : -2.47 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 86 TYR 0.017 0.001 TYR L 100 PHE 0.007 0.001 PHE c 94 TRP 0.025 0.002 TRP H 39 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 3660) covalent geometry : angle 0.69592 ( 4979) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.16395 ( 2) hydrogen bonds : bond 0.18328 ( 125) hydrogen bonds : angle 7.38679 ( 336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: L 100 TYR cc_start: 0.9278 (p90) cc_final: 0.8494 (p90) REVERT: H 7 LEU cc_start: 0.9149 (pt) cc_final: 0.8446 (pt) REVERT: H 54 PHE cc_start: 0.8914 (t80) cc_final: 0.8655 (t80) REVERT: H 76 ASP cc_start: 0.8764 (p0) cc_final: 0.8430 (p0) REVERT: H 113 GLN cc_start: 0.8262 (pm20) cc_final: 0.7923 (pm20) REVERT: C 13 LYS cc_start: 0.8324 (mttt) cc_final: 0.8045 (mttp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0770 time to fit residues: 11.0790 Evaluate side-chains 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 GLN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.076828 restraints weight = 7079.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.079000 restraints weight = 4324.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080435 restraints weight = 3116.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081491 restraints weight = 2516.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081805 restraints weight = 2171.531| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3661 Z= 0.149 Angle : 0.657 8.082 4981 Z= 0.335 Chirality : 0.045 0.158 574 Planarity : 0.004 0.037 641 Dihedral : 4.873 20.626 501 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.51 % Allowed : 14.36 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.38), residues: 461 helix: 0.34 (0.77), residues: 45 sheet: -0.66 (0.39), residues: 188 loop : -2.50 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 86 TYR 0.017 0.001 TYR H 30 PHE 0.009 0.001 PHE L 80 TRP 0.011 0.001 TRP H 39 HIS 0.002 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3660) covalent geometry : angle 0.65718 ( 4979) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.35642 ( 2) hydrogen bonds : bond 0.03950 ( 125) hydrogen bonds : angle 5.64336 ( 336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.160 Fit side-chains REVERT: L 100 TYR cc_start: 0.9298 (p90) cc_final: 0.8253 (p90) REVERT: H 84 MET cc_start: 0.8509 (ptt) cc_final: 0.8082 (ptt) REVERT: H 113 GLN cc_start: 0.8269 (pm20) cc_final: 0.8014 (pm20) REVERT: C 14 ASP cc_start: 0.8425 (p0) cc_final: 0.8078 (p0) REVERT: C 89 TYR cc_start: 0.8937 (m-80) cc_final: 0.8682 (m-10) REVERT: C 123 ASP cc_start: 0.8281 (t0) cc_final: 0.8052 (t70) REVERT: c 46 LYS cc_start: 0.9099 (mttm) cc_final: 0.8882 (mtpp) outliers start: 6 outliers final: 5 residues processed: 125 average time/residue: 0.0725 time to fit residues: 10.8079 Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 GLN C 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.075089 restraints weight = 7086.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.077084 restraints weight = 4449.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.078464 restraints weight = 3259.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079373 restraints weight = 2654.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.079871 restraints weight = 2319.071| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3661 Z= 0.267 Angle : 0.704 8.110 4981 Z= 0.364 Chirality : 0.045 0.154 574 Planarity : 0.004 0.030 641 Dihedral : 5.198 22.802 501 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.53 % Allowed : 17.38 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.38), residues: 461 helix: 0.19 (0.77), residues: 47 sheet: -0.57 (0.40), residues: 184 loop : -2.66 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 86 TYR 0.021 0.001 TYR H 53 PHE 0.009 0.001 PHE L 106 TRP 0.006 0.001 TRP L 44 HIS 0.003 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 3660) covalent geometry : angle 0.70374 ( 4979) SS BOND : bond 0.00736 ( 1) SS BOND : angle 0.96534 ( 2) hydrogen bonds : bond 0.04050 ( 125) hydrogen bonds : angle 5.47568 ( 336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.140 Fit side-chains REVERT: H 84 MET cc_start: 0.8559 (ptt) cc_final: 0.8113 (ptt) REVERT: H 104 ASP cc_start: 0.7924 (m-30) cc_final: 0.7586 (m-30) REVERT: C 14 ASP cc_start: 0.8535 (p0) cc_final: 0.8139 (p0) REVERT: C 37 GLN cc_start: 0.8506 (pt0) cc_final: 0.7969 (pt0) REVERT: C 123 ASP cc_start: 0.8269 (t0) cc_final: 0.7980 (t70) REVERT: c 123 ASP cc_start: 0.7833 (t0) cc_final: 0.7610 (t0) outliers start: 14 outliers final: 13 residues processed: 123 average time/residue: 0.0773 time to fit residues: 11.2790 Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.076637 restraints weight = 6939.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.078629 restraints weight = 4315.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080046 restraints weight = 3153.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080928 restraints weight = 2550.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081629 restraints weight = 2224.513| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3661 Z= 0.189 Angle : 0.677 8.074 4981 Z= 0.350 Chirality : 0.045 0.146 574 Planarity : 0.004 0.031 641 Dihedral : 5.139 21.719 501 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.52 % Allowed : 19.90 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.39), residues: 461 helix: 0.27 (0.76), residues: 47 sheet: -0.78 (0.39), residues: 193 loop : -2.40 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 86 TYR 0.014 0.001 TYR H 53 PHE 0.008 0.001 PHE L 106 TRP 0.005 0.001 TRP L 44 HIS 0.002 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3660) covalent geometry : angle 0.67741 ( 4979) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.73586 ( 2) hydrogen bonds : bond 0.03602 ( 125) hydrogen bonds : angle 5.40124 ( 336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: L 7 MET cc_start: 0.8651 (mmm) cc_final: 0.8268 (mmm) REVERT: L 26 CYS cc_start: 0.8059 (t) cc_final: 0.7564 (t) REVERT: L 30 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8065 (tm-30) REVERT: L 100 TYR cc_start: 0.9184 (p90) cc_final: 0.8687 (p90) REVERT: H 84 MET cc_start: 0.8516 (ptt) cc_final: 0.8195 (ptm) REVERT: H 104 ASP cc_start: 0.7896 (m-30) cc_final: 0.7538 (m-30) REVERT: C 14 ASP cc_start: 0.8330 (p0) cc_final: 0.8000 (p0) REVERT: C 37 GLN cc_start: 0.8392 (pt0) cc_final: 0.8022 (pt0) REVERT: C 123 ASP cc_start: 0.8243 (t0) cc_final: 0.8032 (t70) outliers start: 10 outliers final: 7 residues processed: 122 average time/residue: 0.0753 time to fit residues: 11.0094 Evaluate side-chains 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.0570 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 9 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.078553 restraints weight = 6889.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080605 restraints weight = 4272.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081985 restraints weight = 3103.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082607 restraints weight = 2517.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.083333 restraints weight = 2249.662| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3661 Z= 0.146 Angle : 0.665 7.951 4981 Z= 0.341 Chirality : 0.043 0.143 574 Planarity : 0.004 0.030 641 Dihedral : 4.940 21.761 501 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.78 % Allowed : 21.41 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.39), residues: 461 helix: 0.37 (0.76), residues: 48 sheet: -0.78 (0.39), residues: 194 loop : -2.37 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 86 TYR 0.021 0.001 TYR H 53 PHE 0.006 0.001 PHE L 80 TRP 0.005 0.001 TRP H 111 HIS 0.001 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3660) covalent geometry : angle 0.66531 ( 4979) SS BOND : bond 0.00489 ( 1) SS BOND : angle 0.60280 ( 2) hydrogen bonds : bond 0.03243 ( 125) hydrogen bonds : angle 5.25685 ( 336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: L 7 MET cc_start: 0.8865 (mmm) cc_final: 0.8396 (mmm) REVERT: L 30 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8036 (tm-30) REVERT: L 100 TYR cc_start: 0.9121 (p90) cc_final: 0.8628 (p90) REVERT: H 73 LEU cc_start: 0.8986 (mm) cc_final: 0.8692 (mm) REVERT: H 104 ASP cc_start: 0.7926 (m-30) cc_final: 0.7563 (m-30) REVERT: C 37 GLN cc_start: 0.8175 (pt0) cc_final: 0.7939 (pt0) REVERT: C 47 ARG cc_start: 0.7683 (ptp-110) cc_final: 0.7328 (ptp90) REVERT: C 123 ASP cc_start: 0.8172 (t0) cc_final: 0.7916 (t70) outliers start: 15 outliers final: 10 residues processed: 133 average time/residue: 0.0664 time to fit residues: 10.5020 Evaluate side-chains 127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.099359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.075677 restraints weight = 7000.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077611 restraints weight = 4349.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078900 restraints weight = 3191.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079880 restraints weight = 2612.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080383 restraints weight = 2281.655| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3661 Z= 0.224 Angle : 0.709 7.715 4981 Z= 0.364 Chirality : 0.044 0.152 574 Planarity : 0.004 0.031 641 Dihedral : 5.138 22.459 501 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.79 % Allowed : 22.92 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.39), residues: 461 helix: 0.42 (0.74), residues: 49 sheet: -0.80 (0.39), residues: 194 loop : -2.36 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 86 TYR 0.016 0.001 TYR H 53 PHE 0.007 0.001 PHE L 101 TRP 0.022 0.002 TRP H 39 HIS 0.002 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 3660) covalent geometry : angle 0.70940 ( 4979) SS BOND : bond 0.00555 ( 1) SS BOND : angle 0.72326 ( 2) hydrogen bonds : bond 0.03590 ( 125) hydrogen bonds : angle 5.32186 ( 336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: L 7 MET cc_start: 0.8737 (mmm) cc_final: 0.8451 (mmm) REVERT: L 30 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8016 (tm-30) REVERT: L 100 TYR cc_start: 0.9188 (p90) cc_final: 0.8828 (p90) REVERT: H 84 MET cc_start: 0.8710 (ptt) cc_final: 0.8249 (ptm) REVERT: H 104 ASP cc_start: 0.7835 (m-30) cc_final: 0.7454 (m-30) REVERT: C 14 ASP cc_start: 0.8317 (p0) cc_final: 0.7982 (p0) REVERT: C 47 ARG cc_start: 0.7821 (ptp-110) cc_final: 0.7409 (ptp90) REVERT: C 123 ASP cc_start: 0.8203 (t0) cc_final: 0.7969 (t70) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.0704 time to fit residues: 11.0572 Evaluate side-chains 129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.078780 restraints weight = 7049.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080893 restraints weight = 4287.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082385 restraints weight = 3082.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.083312 restraints weight = 2471.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084032 restraints weight = 2142.800| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3661 Z= 0.131 Angle : 0.685 7.719 4981 Z= 0.350 Chirality : 0.043 0.141 574 Planarity : 0.004 0.033 641 Dihedral : 4.846 21.125 501 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.53 % Allowed : 23.93 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.39), residues: 461 helix: 0.55 (0.75), residues: 48 sheet: -0.59 (0.40), residues: 189 loop : -2.39 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 86 TYR 0.015 0.001 TYR H 53 PHE 0.007 0.001 PHE L 80 TRP 0.018 0.001 TRP H 39 HIS 0.001 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3660) covalent geometry : angle 0.68480 ( 4979) SS BOND : bond 0.00556 ( 1) SS BOND : angle 1.36580 ( 2) hydrogen bonds : bond 0.03127 ( 125) hydrogen bonds : angle 5.06913 ( 336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: L 30 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7981 (tm-30) REVERT: L 100 TYR cc_start: 0.9208 (p90) cc_final: 0.8859 (p90) REVERT: H 84 MET cc_start: 0.8754 (ptt) cc_final: 0.8261 (ptm) REVERT: H 88 ASN cc_start: 0.8477 (t0) cc_final: 0.7484 (m-40) REVERT: H 89 LEU cc_start: 0.8768 (mt) cc_final: 0.7663 (pp) REVERT: H 104 ASP cc_start: 0.8028 (m-30) cc_final: 0.7650 (m-30) REVERT: C 37 GLN cc_start: 0.7904 (pt0) cc_final: 0.7544 (pt0) REVERT: C 47 ARG cc_start: 0.7717 (ptp-110) cc_final: 0.7265 (ptp90) REVERT: C 95 SER cc_start: 0.8704 (t) cc_final: 0.8460 (t) REVERT: C 123 ASP cc_start: 0.8216 (t0) cc_final: 0.7952 (t70) outliers start: 14 outliers final: 12 residues processed: 131 average time/residue: 0.0702 time to fit residues: 11.0929 Evaluate side-chains 129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.097626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.073892 restraints weight = 7192.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.075782 restraints weight = 4461.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.077120 restraints weight = 3271.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077831 restraints weight = 2669.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.078498 restraints weight = 2366.694| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3661 Z= 0.326 Angle : 0.798 9.946 4981 Z= 0.412 Chirality : 0.047 0.155 574 Planarity : 0.005 0.044 641 Dihedral : 5.367 23.226 501 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 4.28 % Allowed : 23.43 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.39), residues: 461 helix: 0.38 (0.75), residues: 47 sheet: -0.82 (0.39), residues: 196 loop : -2.34 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 86 TYR 0.018 0.001 TYR H 53 PHE 0.010 0.002 PHE C 10 TRP 0.012 0.002 TRP H 39 HIS 0.003 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 3660) covalent geometry : angle 0.79721 ( 4979) SS BOND : bond 0.00796 ( 1) SS BOND : angle 1.65635 ( 2) hydrogen bonds : bond 0.04052 ( 125) hydrogen bonds : angle 5.36961 ( 336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: L 100 TYR cc_start: 0.9278 (p90) cc_final: 0.8975 (p90) REVERT: H 84 MET cc_start: 0.8780 (ptt) cc_final: 0.8330 (ptm) REVERT: H 104 ASP cc_start: 0.8009 (m-30) cc_final: 0.7666 (m-30) REVERT: C 14 ASP cc_start: 0.8367 (p0) cc_final: 0.8062 (p0) REVERT: C 47 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7467 (ptp90) REVERT: C 123 ASP cc_start: 0.8319 (t0) cc_final: 0.8085 (t70) outliers start: 17 outliers final: 15 residues processed: 120 average time/residue: 0.0699 time to fit residues: 9.9801 Evaluate side-chains 125 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.077834 restraints weight = 6915.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079877 restraints weight = 4219.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081313 restraints weight = 3069.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.082056 restraints weight = 2464.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082909 restraints weight = 2166.280| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3661 Z= 0.145 Angle : 0.726 8.419 4981 Z= 0.372 Chirality : 0.044 0.143 574 Planarity : 0.004 0.032 641 Dihedral : 4.974 21.340 501 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.53 % Allowed : 24.94 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.39), residues: 461 helix: 0.57 (0.75), residues: 48 sheet: -0.59 (0.40), residues: 194 loop : -2.33 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 86 TYR 0.015 0.001 TYR H 53 PHE 0.007 0.001 PHE L 80 TRP 0.018 0.002 TRP H 39 HIS 0.001 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3660) covalent geometry : angle 0.72562 ( 4979) SS BOND : bond 0.00553 ( 1) SS BOND : angle 1.29711 ( 2) hydrogen bonds : bond 0.03291 ( 125) hydrogen bonds : angle 5.13389 ( 336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.170 Fit side-chains REVERT: L 30 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7983 (tm-30) REVERT: L 100 TYR cc_start: 0.9208 (p90) cc_final: 0.8993 (p90) REVERT: H 73 LEU cc_start: 0.8866 (mm) cc_final: 0.8546 (mm) REVERT: H 84 MET cc_start: 0.8744 (ptt) cc_final: 0.8309 (ptm) REVERT: H 88 ASN cc_start: 0.8427 (t0) cc_final: 0.7692 (m-40) REVERT: H 104 ASP cc_start: 0.7927 (m-30) cc_final: 0.7512 (m-30) REVERT: C 47 ARG cc_start: 0.7736 (ptp-110) cc_final: 0.7356 (ptp90) REVERT: C 123 ASP cc_start: 0.8191 (t0) cc_final: 0.7946 (t70) outliers start: 14 outliers final: 11 residues processed: 126 average time/residue: 0.0747 time to fit residues: 11.2358 Evaluate side-chains 122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 0.0060 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.077012 restraints weight = 7057.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079012 restraints weight = 4340.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080339 restraints weight = 3152.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.081105 restraints weight = 2561.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081889 restraints weight = 2267.303| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3661 Z= 0.183 Angle : 0.759 8.153 4981 Z= 0.389 Chirality : 0.044 0.148 574 Planarity : 0.005 0.054 641 Dihedral : 5.106 21.239 501 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.52 % Allowed : 26.45 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.39), residues: 461 helix: 0.70 (0.74), residues: 47 sheet: -0.43 (0.41), residues: 192 loop : -2.37 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 86 TYR 0.017 0.001 TYR H 53 PHE 0.007 0.001 PHE L 101 TRP 0.015 0.001 TRP H 39 HIS 0.002 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 3660) covalent geometry : angle 0.75862 ( 4979) SS BOND : bond 0.00580 ( 1) SS BOND : angle 1.45077 ( 2) hydrogen bonds : bond 0.03391 ( 125) hydrogen bonds : angle 5.07498 ( 336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.080 Fit side-chains REVERT: L 30 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8041 (tm-30) REVERT: L 100 TYR cc_start: 0.9167 (p90) cc_final: 0.8888 (p90) REVERT: H 9 GLN cc_start: 0.8657 (tp40) cc_final: 0.7964 (tt0) REVERT: H 73 LEU cc_start: 0.8879 (mm) cc_final: 0.8581 (mm) REVERT: H 84 MET cc_start: 0.8713 (ptt) cc_final: 0.8325 (ptm) REVERT: H 88 ASN cc_start: 0.8407 (t0) cc_final: 0.7616 (m-40) REVERT: H 104 ASP cc_start: 0.7847 (m-30) cc_final: 0.7478 (m-30) REVERT: C 14 ASP cc_start: 0.8360 (p0) cc_final: 0.7956 (p0) REVERT: C 47 ARG cc_start: 0.7665 (ptp-110) cc_final: 0.7324 (ptp90) REVERT: C 95 SER cc_start: 0.8697 (t) cc_final: 0.8457 (t) REVERT: C 123 ASP cc_start: 0.8184 (t0) cc_final: 0.7956 (t70) outliers start: 10 outliers final: 10 residues processed: 123 average time/residue: 0.0658 time to fit residues: 9.6226 Evaluate side-chains 125 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.102569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.078295 restraints weight = 6922.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080382 restraints weight = 4251.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.081787 restraints weight = 3075.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082741 restraints weight = 2492.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083439 restraints weight = 2165.722| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3661 Z= 0.144 Angle : 0.731 7.773 4981 Z= 0.374 Chirality : 0.043 0.139 574 Planarity : 0.004 0.048 641 Dihedral : 4.965 21.846 501 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.02 % Allowed : 26.45 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.40), residues: 461 helix: 0.65 (0.74), residues: 48 sheet: -0.39 (0.41), residues: 194 loop : -2.32 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 86 TYR 0.017 0.001 TYR H 53 PHE 0.007 0.001 PHE L 80 TRP 0.016 0.001 TRP H 39 HIS 0.001 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3660) covalent geometry : angle 0.73105 ( 4979) SS BOND : bond 0.00551 ( 1) SS BOND : angle 1.29266 ( 2) hydrogen bonds : bond 0.03139 ( 125) hydrogen bonds : angle 4.93517 ( 336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 708.87 seconds wall clock time: 12 minutes 55.03 seconds (775.03 seconds total)