Starting phenix.real_space_refine on Wed Mar 5 21:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5u_37304/03_2025/8w5u_37304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5u_37304/03_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_37304/03_2025/8w5u_37304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5u_37304/03_2025/8w5u_37304.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5u_37304/03_2025/8w5u_37304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5u_37304/03_2025/8w5u_37304.cif" } resolution = 3.9 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= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.58, per 1000 atoms: 0.72 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: 0.75 Conformation dependent library (CDL) restraints added in 431.4 milliseconds 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: 0.44 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: 0.77 Time building geometry restraints manager: 0.91 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: 0.530 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- 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 3660 Z= 0.347 Angle : 0.696 7.879 4979 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 (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: -2.34 (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 TRP 0.025 0.002 TRP H 39 HIS 0.002 0.001 HIS H 38 PHE 0.007 0.001 PHE c 94 TYR 0.017 0.001 TYR L 100 ARG 0.009 0.001 ARG C 86 *********************** 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 : 0.376 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: 0.1854 time to fit residues: 26.6632 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 GLN H 6 GLN C 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076922 restraints weight = 6952.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078986 restraints weight = 4276.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080452 restraints weight = 3129.349| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3660 Z= 0.222 Angle : 0.652 8.019 4979 Z= 0.332 Chirality : 0.045 0.158 574 Planarity : 0.004 0.036 641 Dihedral : 4.844 20.147 501 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.51 % Allowed : 14.61 % Favored : 83.88 % 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: -2.12 (0.38), residues: 461 helix: 0.32 (0.77), residues: 45 sheet: -0.63 (0.40), residues: 187 loop : -2.51 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 39 HIS 0.002 0.001 HIS H 44 PHE 0.010 0.001 PHE L 80 TYR 0.017 0.001 TYR H 30 ARG 0.004 0.000 ARG C 86 *********************** 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 129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.393 Fit side-chains REVERT: L 30 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8006 (tm-30) REVERT: L 100 TYR cc_start: 0.9263 (p90) cc_final: 0.8268 (p90) REVERT: H 84 MET cc_start: 0.8528 (ptt) cc_final: 0.8090 (ptt) REVERT: H 113 GLN cc_start: 0.8263 (pm20) cc_final: 0.8018 (pm20) REVERT: C 14 ASP cc_start: 0.8423 (p0) cc_final: 0.8085 (p0) REVERT: C 123 ASP cc_start: 0.8217 (t0) cc_final: 0.7985 (t70) REVERT: c 46 LYS cc_start: 0.9099 (mttm) cc_final: 0.8878 (mtpp) REVERT: c 103 GLU cc_start: 0.8301 (pp20) cc_final: 0.8097 (pp20) outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 0.1792 time to fit residues: 26.2036 Evaluate side-chains 114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 34 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.100254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076500 restraints weight = 6902.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078534 restraints weight = 4217.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079983 restraints weight = 3054.751| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3660 Z= 0.292 Angle : 0.656 7.939 4979 Z= 0.338 Chirality : 0.044 0.153 574 Planarity : 0.004 0.029 641 Dihedral : 4.985 21.718 501 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.27 % Allowed : 16.88 % Favored : 80.86 % 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: -2.06 (0.38), residues: 461 helix: 0.20 (0.77), residues: 47 sheet: -0.38 (0.40), residues: 182 loop : -2.61 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 39 HIS 0.002 0.001 HIS H 44 PHE 0.009 0.001 PHE L 106 TYR 0.021 0.001 TYR H 53 ARG 0.003 0.001 ARG C 86 *********************** 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: 9 poor density : 122 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: H 84 MET cc_start: 0.8518 (ptt) cc_final: 0.8156 (ptt) REVERT: H 104 ASP cc_start: 0.7925 (m-30) cc_final: 0.7551 (m-30) REVERT: H 113 GLN cc_start: 0.8375 (pm20) cc_final: 0.8170 (pm20) REVERT: C 14 ASP cc_start: 0.8536 (p0) cc_final: 0.8052 (p0) REVERT: C 37 GLN cc_start: 0.8502 (pt0) cc_final: 0.7988 (pt0) REVERT: C 69 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7875 (mm110) REVERT: C 123 ASP cc_start: 0.8261 (t0) cc_final: 0.8012 (t70) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 0.1811 time to fit residues: 27.0730 Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 83 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 9 GLN L 48 ASN C 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.080001 restraints weight = 6955.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082110 restraints weight = 4241.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083605 restraints weight = 3062.815| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3660 Z= 0.188 Angle : 0.653 7.774 4979 Z= 0.332 Chirality : 0.043 0.141 574 Planarity : 0.004 0.038 641 Dihedral : 4.767 20.548 501 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.53 % Allowed : 18.64 % Favored : 77.83 % 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: -1.98 (0.38), residues: 461 helix: 0.44 (0.77), residues: 47 sheet: -0.36 (0.40), residues: 185 loop : -2.60 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.001 0.000 HIS H 44 PHE 0.008 0.001 PHE L 80 TYR 0.021 0.001 TYR H 53 ARG 0.005 0.001 ARG L 70 *********************** 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 139 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.390 Fit side-chains REVERT: L 7 MET cc_start: 0.8907 (mmm) cc_final: 0.8205 (mmm) REVERT: L 30 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8004 (tm-30) REVERT: L 56 LEU cc_start: 0.9376 (mm) cc_final: 0.9171 (mm) REVERT: H 39 TRP cc_start: 0.9236 (m100) cc_final: 0.9033 (m100) REVERT: H 84 MET cc_start: 0.8495 (ptt) cc_final: 0.8229 (ptt) REVERT: H 89 LEU cc_start: 0.8644 (mt) cc_final: 0.7984 (pp) REVERT: H 104 ASP cc_start: 0.8033 (m-30) cc_final: 0.7676 (m-30) REVERT: H 113 GLN cc_start: 0.8426 (pm20) cc_final: 0.8213 (pm20) REVERT: C 14 ASP cc_start: 0.8503 (p0) cc_final: 0.8192 (p0) REVERT: C 37 GLN cc_start: 0.8173 (pt0) cc_final: 0.7917 (pt0) REVERT: C 69 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7804 (mm110) outliers start: 14 outliers final: 9 residues processed: 132 average time/residue: 0.1807 time to fit residues: 28.2214 Evaluate side-chains 123 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 52 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 38 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.076195 restraints weight = 7043.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078185 restraints weight = 4362.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079581 restraints weight = 3190.054| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3660 Z= 0.341 Angle : 0.689 7.464 4979 Z= 0.354 Chirality : 0.044 0.155 574 Planarity : 0.004 0.028 641 Dihedral : 5.035 21.935 501 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.53 % Allowed : 21.66 % 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 (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: -2.03 (0.38), residues: 461 helix: 0.31 (0.73), residues: 49 sheet: -0.55 (0.40), residues: 186 loop : -2.49 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 44 HIS 0.002 0.001 HIS H 44 PHE 0.009 0.001 PHE L 106 TYR 0.022 0.001 TYR H 53 ARG 0.005 0.001 ARG C 86 *********************** 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 134 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.339 Fit side-chains REVERT: L 7 MET cc_start: 0.8862 (mmm) cc_final: 0.8405 (mmm) REVERT: L 30 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7990 (tm-30) REVERT: L 100 TYR cc_start: 0.9177 (p90) cc_final: 0.8929 (p90) REVERT: H 39 TRP cc_start: 0.9267 (m100) cc_final: 0.9054 (m100) REVERT: H 73 LEU cc_start: 0.9004 (mm) cc_final: 0.8723 (mm) REVERT: H 104 ASP cc_start: 0.7878 (m-30) cc_final: 0.7538 (m-30) REVERT: C 14 ASP cc_start: 0.8375 (p0) cc_final: 0.8031 (p0) REVERT: C 37 GLN cc_start: 0.8318 (pt0) cc_final: 0.8063 (pt0) REVERT: C 47 ARG cc_start: 0.7796 (ptp-110) cc_final: 0.7439 (ptp90) REVERT: C 123 ASP cc_start: 0.8156 (t0) cc_final: 0.7928 (t70) outliers start: 14 outliers final: 12 residues processed: 126 average time/residue: 0.1779 time to fit residues: 26.6392 Evaluate side-chains 127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 67 VAL 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 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 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 16 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 9 optimal weight: 6.9990 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN 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 = 0.102293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078421 restraints weight = 7070.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.080501 restraints weight = 4305.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.082008 restraints weight = 3105.760| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3660 Z= 0.238 Angle : 0.679 7.301 4979 Z= 0.348 Chirality : 0.044 0.147 574 Planarity : 0.004 0.031 641 Dihedral : 4.886 20.662 501 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.53 % Allowed : 21.91 % Favored : 73.55 % 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: -1.86 (0.39), residues: 461 helix: 0.56 (0.74), residues: 49 sheet: -0.41 (0.40), residues: 185 loop : -2.42 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 44 HIS 0.001 0.000 HIS H 44 PHE 0.009 0.001 PHE L 106 TYR 0.014 0.001 TYR H 53 ARG 0.005 0.001 ARG C 86 *********************** 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 145 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.407 Fit side-chains REVERT: L 7 MET cc_start: 0.8918 (mmm) cc_final: 0.8636 (mmm) REVERT: L 30 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8016 (tm-30) REVERT: L 100 TYR cc_start: 0.9162 (p90) cc_final: 0.8873 (p90) REVERT: H 39 TRP cc_start: 0.9189 (m100) cc_final: 0.8714 (m100) REVERT: H 73 LEU cc_start: 0.8970 (mm) cc_final: 0.8625 (mm) REVERT: H 84 MET cc_start: 0.8651 (ptt) cc_final: 0.8279 (ptp) REVERT: H 104 ASP cc_start: 0.7972 (m-30) cc_final: 0.7605 (m-30) REVERT: C 47 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7435 (ptp90) REVERT: C 69 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7909 (mm-40) REVERT: C 123 ASP cc_start: 0.8165 (t0) cc_final: 0.7923 (t70) outliers start: 18 outliers final: 13 residues processed: 136 average time/residue: 0.1774 time to fit residues: 28.6999 Evaluate side-chains 128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 21 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.103572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.079685 restraints weight = 6949.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081793 restraints weight = 4216.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083295 restraints weight = 3032.222| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3660 Z= 0.205 Angle : 0.674 6.968 4979 Z= 0.345 Chirality : 0.043 0.142 574 Planarity : 0.004 0.030 641 Dihedral : 4.713 20.413 501 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.03 % Allowed : 22.92 % Favored : 73.05 % 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: -1.73 (0.39), residues: 461 helix: 0.52 (0.74), residues: 47 sheet: -0.10 (0.42), residues: 177 loop : -2.43 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 111 HIS 0.001 0.000 HIS H 44 PHE 0.007 0.001 PHE L 80 TYR 0.014 0.001 TYR H 53 ARG 0.007 0.001 ARG c 86 *********************** 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 141 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.426 Fit side-chains REVERT: L 7 MET cc_start: 0.8900 (mmm) cc_final: 0.8618 (mmm) REVERT: L 30 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8007 (tm-30) REVERT: L 100 TYR cc_start: 0.9131 (p90) cc_final: 0.8850 (p90) REVERT: H 34 ASP cc_start: 0.7988 (t0) cc_final: 0.7779 (t0) REVERT: H 39 TRP cc_start: 0.9187 (m100) cc_final: 0.8871 (m100) REVERT: H 73 LEU cc_start: 0.8912 (mm) cc_final: 0.8631 (mm) REVERT: H 88 ASN cc_start: 0.8449 (t0) cc_final: 0.7590 (m-40) REVERT: H 89 LEU cc_start: 0.8729 (mt) cc_final: 0.7692 (pp) REVERT: H 104 ASP cc_start: 0.7950 (m-30) cc_final: 0.7534 (m-30) REVERT: C 47 ARG cc_start: 0.7622 (ptp-110) cc_final: 0.7308 (ptp90) REVERT: C 95 SER cc_start: 0.8677 (t) cc_final: 0.8429 (t) REVERT: C 123 ASP cc_start: 0.8159 (t0) cc_final: 0.7929 (t70) outliers start: 16 outliers final: 11 residues processed: 132 average time/residue: 0.1744 time to fit residues: 27.6453 Evaluate side-chains 131 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 118 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 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 = 0.3327 r_free = 0.3327 target = 0.101078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.077071 restraints weight = 6947.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079134 restraints weight = 4246.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080501 restraints weight = 3061.784| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3660 Z= 0.344 Angle : 0.727 6.453 4979 Z= 0.378 Chirality : 0.044 0.151 574 Planarity : 0.004 0.037 641 Dihedral : 5.062 21.006 501 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.79 % Allowed : 23.17 % Favored : 72.04 % 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: -1.88 (0.39), residues: 461 helix: 0.43 (0.72), residues: 49 sheet: -0.40 (0.40), residues: 186 loop : -2.44 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.002 0.001 HIS H 44 PHE 0.012 0.001 PHE L 106 TYR 0.022 0.001 TYR H 53 ARG 0.007 0.001 ARG c 86 *********************** 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 135 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.422 Fit side-chains REVERT: L 30 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7990 (tm-30) REVERT: L 100 TYR cc_start: 0.9219 (p90) cc_final: 0.8831 (p90) REVERT: H 9 GLN cc_start: 0.8547 (tp40) cc_final: 0.7721 (tt0) REVERT: H 73 LEU cc_start: 0.8960 (mm) cc_final: 0.8746 (mm) REVERT: H 84 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7805 (pmm) REVERT: H 104 ASP cc_start: 0.7981 (m-30) cc_final: 0.7610 (m-30) REVERT: C 47 ARG cc_start: 0.7779 (ptp-110) cc_final: 0.7384 (ptp90) REVERT: C 69 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7831 (mm110) REVERT: C 95 SER cc_start: 0.8696 (t) cc_final: 0.8464 (t) REVERT: C 123 ASP cc_start: 0.8242 (t0) cc_final: 0.8016 (t70) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.1721 time to fit residues: 26.0526 Evaluate side-chains 127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 83 TYR Chi-restraints excluded: chain H residue 84 MET 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 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 46 LYS 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 35 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.103521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.079379 restraints weight = 6927.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.081380 restraints weight = 4318.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082798 restraints weight = 3174.205| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3660 Z= 0.215 Angle : 0.728 9.639 4979 Z= 0.372 Chirality : 0.044 0.145 574 Planarity : 0.004 0.030 641 Dihedral : 4.866 19.966 501 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.53 % Allowed : 24.69 % Favored : 71.79 % 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: -1.66 (0.39), residues: 461 helix: 0.79 (0.73), residues: 49 sheet: -0.14 (0.41), residues: 184 loop : -2.44 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 39 HIS 0.001 0.000 HIS H 44 PHE 0.008 0.001 PHE L 106 TYR 0.015 0.001 TYR H 53 ARG 0.009 0.001 ARG c 86 *********************** 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 139 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.340 Fit side-chains REVERT: L 7 MET cc_start: 0.8836 (mmm) cc_final: 0.8482 (mmm) REVERT: L 30 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8016 (tm-30) REVERT: H 9 GLN cc_start: 0.8415 (tp40) cc_final: 0.7885 (tt0) REVERT: H 88 ASN cc_start: 0.8488 (t0) cc_final: 0.7615 (m-40) REVERT: H 89 LEU cc_start: 0.8711 (mt) cc_final: 0.7669 (pp) REVERT: H 104 ASP cc_start: 0.7801 (m-30) cc_final: 0.7388 (m-30) REVERT: C 47 ARG cc_start: 0.7650 (ptp-110) cc_final: 0.7322 (ptp90) REVERT: C 69 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7961 (mm110) REVERT: C 95 SER cc_start: 0.8666 (t) cc_final: 0.8424 (t) REVERT: C 123 ASP cc_start: 0.8105 (t0) cc_final: 0.7897 (t70) outliers start: 14 outliers final: 10 residues processed: 132 average time/residue: 0.1679 time to fit residues: 26.3389 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 : 0.338 ------------------------------------------------------------------------------- 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 101 THR 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 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.101757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077333 restraints weight = 7019.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.079290 restraints weight = 4320.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.080746 restraints weight = 3159.456| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3660 Z= 0.331 Angle : 0.763 8.660 4979 Z= 0.392 Chirality : 0.045 0.147 574 Planarity : 0.005 0.058 641 Dihedral : 5.197 20.783 501 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.77 % Allowed : 25.94 % Favored : 71.28 % 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: -1.79 (0.39), residues: 461 helix: 0.45 (0.73), residues: 48 sheet: -0.17 (0.41), residues: 178 loop : -2.47 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 39 HIS 0.002 0.001 HIS H 44 PHE 0.010 0.001 PHE L 71 TYR 0.023 0.001 TYR H 53 ARG 0.010 0.001 ARG C 86 ********************** 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 132 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.412 Fit side-chains REVERT: L 7 MET cc_start: 0.8889 (mmm) cc_final: 0.8564 (mmm) REVERT: L 30 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7960 (tm-30) REVERT: L 56 LEU cc_start: 0.9333 (mp) cc_final: 0.9100 (mp) REVERT: H 9 GLN cc_start: 0.8529 (tp40) cc_final: 0.7820 (tt0) REVERT: H 88 ASN cc_start: 0.8451 (t0) cc_final: 0.7711 (m-40) REVERT: H 104 ASP cc_start: 0.7949 (m-30) cc_final: 0.7571 (m-30) REVERT: C 47 ARG cc_start: 0.7737 (ptp-110) cc_final: 0.7360 (ptp90) REVERT: C 69 GLN cc_start: 0.8236 (mm-40) cc_final: 0.8011 (mm110) REVERT: C 95 SER cc_start: 0.8672 (t) cc_final: 0.8434 (t) REVERT: C 123 ASP cc_start: 0.8208 (t0) cc_final: 0.7996 (t70) outliers start: 11 outliers final: 10 residues processed: 126 average time/residue: 0.1729 time to fit residues: 26.0559 Evaluate side-chains 124 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 101 THR 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 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.098664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.074494 restraints weight = 6995.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.076421 restraints weight = 4321.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.077683 restraints weight = 3179.981| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3660 Z= 0.439 Angle : 0.812 8.224 4979 Z= 0.422 Chirality : 0.046 0.153 574 Planarity : 0.005 0.064 641 Dihedral : 5.602 21.678 501 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.77 % Allowed : 26.45 % Favored : 70.78 % 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: -1.91 (0.39), residues: 461 helix: 0.63 (0.73), residues: 48 sheet: -0.43 (0.40), residues: 185 loop : -2.49 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP H 39 HIS 0.003 0.001 HIS H 44 PHE 0.013 0.002 PHE L 106 TYR 0.021 0.002 TYR H 53 ARG 0.011 0.001 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.68 seconds wall clock time: 25 minutes 30.33 seconds (1530.33 seconds total)