Starting phenix.real_space_refine on Sat Apr 26 22:27:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5u_37304/04_2025/8w5u_37304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5u_37304/04_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_37304/04_2025/8w5u_37304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5u_37304/04_2025/8w5u_37304.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5u_37304/04_2025/8w5u_37304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5u_37304/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.10, per 1000 atoms: 0.86 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: 0.97 Conformation dependent library (CDL) restraints added in 462.3 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: 0.42 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: 0.83 Time building geometry restraints manager: 1.17 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: 0.580 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.210 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.18328 ( 125) hydrogen bonds : angle 7.38679 ( 336) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.16395 ( 2) covalent geometry : bond 0.00525 ( 3660) covalent geometry : angle 0.69592 ( 4979) *********************** 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 : 0.399 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: 0.1906 time to fit residues: 27.3391 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 : 0.433 ------------------------------------------------------------------------------- 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: 4.9990 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 3661 Z= 0.146 Angle : 0.652 8.019 4981 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 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 125) hydrogen bonds : angle 5.61365 ( 336) SS BOND : bond 0.00453 ( 1) SS BOND : angle 0.45825 ( 2) covalent geometry : bond 0.00333 ( 3660) covalent geometry : angle 0.65207 ( 4979) *********************** 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 : 0.440 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: 0.1923 time to fit residues: 28.0483 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 : 0.438 ------------------------------------------------------------------------------- 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 3661 Z= 0.193 Angle : 0.657 7.939 4981 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 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 125) hydrogen bonds : angle 5.37466 ( 336) SS BOND : bond 0.00880 ( 1) SS BOND : angle 1.05500 ( 2) covalent geometry : bond 0.00441 ( 3660) covalent geometry : angle 0.65644 ( 4979) *********************** 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 : 0.390 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: 0.1795 time to fit residues: 26.7973 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 : 0.442 ------------------------------------------------------------------------------- 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 3661 Z= 0.121 Angle : 0.653 7.774 4981 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 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 125) hydrogen bonds : angle 5.19127 ( 336) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.81606 ( 2) covalent geometry : bond 0.00282 ( 3660) covalent geometry : angle 0.65301 ( 4979) *********************** 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 : 0.395 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: 0.1884 time to fit residues: 29.4063 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 : 0.350 ------------------------------------------------------------------------------- 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 3661 Z= 0.226 Angle : 0.689 7.464 4981 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 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 125) hydrogen bonds : angle 5.26920 ( 336) SS BOND : bond 0.00990 ( 1) SS BOND : angle 0.50269 ( 2) covalent geometry : bond 0.00516 ( 3660) covalent geometry : angle 0.68870 ( 4979) *********************** 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 : 0.438 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: 0.1813 time to fit residues: 27.1425 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 : 0.407 ------------------------------------------------------------------------------- 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 3661 Z= 0.153 Angle : 0.679 7.301 4981 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 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 125) hydrogen bonds : angle 5.13497 ( 336) SS BOND : bond 0.00390 ( 1) SS BOND : angle 0.60902 ( 2) covalent geometry : bond 0.00358 ( 3660) covalent geometry : angle 0.67867 ( 4979) *********************** 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 : 0.434 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: 0.1785 time to fit residues: 28.9582 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 : 0.407 ------------------------------------------------------------------------------- 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: 0.7980 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: 10.0000 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.105607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.081743 restraints weight = 6923.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083786 restraints weight = 4183.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084994 restraints weight = 3023.521| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3661 Z= 0.119 Angle : 0.674 6.765 4981 Z= 0.345 Chirality : 0.042 0.138 574 Planarity : 0.004 0.031 641 Dihedral : 4.604 19.582 501 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.78 % Allowed : 23.17 % 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: -1.68 (0.39), residues: 461 helix: 0.41 (0.73), residues: 48 sheet: -0.02 (0.42), residues: 177 loop : -2.42 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 111 HIS 0.000 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 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 125) hydrogen bonds : angle 4.91653 ( 336) SS BOND : bond 0.00617 ( 1) SS BOND : angle 0.79793 ( 2) covalent geometry : bond 0.00283 ( 3660) covalent geometry : angle 0.67390 ( 4979) *********************** 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 145 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.429 Fit side-chains REVERT: L 7 MET cc_start: 0.8981 (mmm) cc_final: 0.8653 (mmm) REVERT: L 30 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8093 (tm-30) REVERT: L 100 TYR cc_start: 0.9091 (p90) cc_final: 0.8844 (p90) REVERT: H 39 TRP cc_start: 0.9153 (m100) cc_final: 0.8896 (m100) REVERT: H 73 LEU cc_start: 0.8720 (mm) cc_final: 0.8433 (mm) REVERT: H 88 ASN cc_start: 0.8453 (t0) cc_final: 0.7649 (m-40) REVERT: H 89 LEU cc_start: 0.8673 (mt) cc_final: 0.7679 (pp) REVERT: H 104 ASP cc_start: 0.7987 (m-30) cc_final: 0.7624 (m-30) REVERT: C 95 SER cc_start: 0.8658 (t) cc_final: 0.8421 (t) REVERT: C 128 LEU cc_start: 0.9341 (mt) cc_final: 0.8871 (mt) REVERT: c 52 VAL cc_start: 0.9512 (OUTLIER) cc_final: 0.9305 (m) outliers start: 15 outliers final: 9 residues processed: 136 average time/residue: 0.1620 time to fit residues: 26.5521 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 : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 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 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 26 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** c 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.075552 restraints weight = 7023.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077538 restraints weight = 4368.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078896 restraints weight = 3186.826| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3661 Z= 0.279 Angle : 0.767 6.253 4981 Z= 0.398 Chirality : 0.045 0.153 574 Planarity : 0.005 0.055 641 Dihedral : 5.186 22.715 501 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.79 % Allowed : 23.93 % 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: -1.93 (0.39), residues: 461 helix: 0.49 (0.73), residues: 47 sheet: -0.47 (0.40), residues: 187 loop : -2.45 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 39 HIS 0.003 0.001 HIS H 44 PHE 0.013 0.002 PHE L 106 TYR 0.022 0.001 TYR H 53 ARG 0.008 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 125) hydrogen bonds : angle 5.30112 ( 336) SS BOND : bond 0.00696 ( 1) SS BOND : angle 1.14501 ( 2) covalent geometry : bond 0.00638 ( 3660) covalent geometry : angle 0.76640 ( 4979) *********************** 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 137 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.443 Fit side-chains REVERT: L 30 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7940 (tm-30) REVERT: L 100 TYR cc_start: 0.9233 (p90) cc_final: 0.8842 (p90) REVERT: H 39 TRP cc_start: 0.9162 (m100) cc_final: 0.8747 (m100) REVERT: H 84 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7358 (pmm) REVERT: H 104 ASP cc_start: 0.7958 (m-30) cc_final: 0.7574 (m-30) REVERT: C 14 ASP cc_start: 0.8228 (p0) cc_final: 0.7842 (p0) REVERT: C 47 ARG cc_start: 0.7794 (ptp-110) cc_final: 0.7410 (ptp90) REVERT: C 69 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7860 (mm110) outliers start: 19 outliers final: 14 residues processed: 128 average time/residue: 0.1777 time to fit residues: 27.0788 Evaluate side-chains 126 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 50 VAL 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 35 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.103206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.078661 restraints weight = 6915.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080698 restraints weight = 4176.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082218 restraints weight = 3027.929| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2510 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= 0.143 Angle : 0.751 9.554 4981 Z= 0.377 Chirality : 0.044 0.144 574 Planarity : 0.004 0.047 641 Dihedral : 4.951 19.943 501 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.53 % Allowed : 26.95 % Favored : 69.52 % 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: -1.72 (0.39), residues: 461 helix: 0.65 (0.74), residues: 47 sheet: -0.17 (0.41), residues: 184 loop : -2.45 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 39 HIS 0.001 0.000 HIS H 44 PHE 0.009 0.001 PHE L 106 TYR 0.016 0.001 TYR H 53 ARG 0.008 0.001 ARG c 86 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 125) hydrogen bonds : angle 5.10732 ( 336) SS BOND : bond 0.00665 ( 1) SS BOND : angle 1.58934 ( 2) covalent geometry : bond 0.00340 ( 3660) covalent geometry : angle 0.75013 ( 4979) *********************** 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 136 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.435 Fit side-chains REVERT: L 7 MET cc_start: 0.8879 (mmm) cc_final: 0.8519 (mmm) REVERT: L 30 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7978 (tm-30) REVERT: L 100 TYR cc_start: 0.9191 (p90) cc_final: 0.8923 (p90) REVERT: H 9 GLN cc_start: 0.8547 (tp40) cc_final: 0.7891 (tt0) REVERT: H 88 ASN cc_start: 0.8534 (t0) cc_final: 0.7685 (m-40) REVERT: H 89 LEU cc_start: 0.8749 (mt) cc_final: 0.7682 (pp) REVERT: H 104 ASP cc_start: 0.8098 (m-30) cc_final: 0.7707 (m-30) REVERT: C 47 ARG cc_start: 0.7663 (ptp-110) cc_final: 0.7259 (ptp90) REVERT: C 69 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7917 (mm110) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.1748 time to fit residues: 26.8209 Evaluate side-chains 127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.101507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.077431 restraints weight = 6996.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.079543 restraints weight = 4136.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.081077 restraints weight = 2944.145| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3661 Z= 0.190 Angle : 0.774 8.797 4981 Z= 0.392 Chirality : 0.044 0.145 574 Planarity : 0.005 0.071 641 Dihedral : 5.136 20.859 501 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.53 % Allowed : 27.20 % Favored : 69.27 % 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: -1.67 (0.39), residues: 461 helix: 0.70 (0.71), residues: 49 sheet: -0.18 (0.41), residues: 184 loop : -2.40 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 39 HIS 0.002 0.001 HIS H 44 PHE 0.008 0.001 PHE L 106 TYR 0.018 0.001 TYR H 53 ARG 0.008 0.001 ARG c 86 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 125) hydrogen bonds : angle 5.18628 ( 336) SS BOND : bond 0.00852 ( 1) SS BOND : angle 1.88942 ( 2) covalent geometry : bond 0.00444 ( 3660) covalent geometry : angle 0.77281 ( 4979) ********************** 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 135 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.459 Fit side-chains REVERT: L 7 MET cc_start: 0.8884 (mmm) cc_final: 0.8452 (mmm) REVERT: L 30 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8002 (tm-30) REVERT: L 100 TYR cc_start: 0.9220 (p90) cc_final: 0.8828 (p90) REVERT: H 9 GLN cc_start: 0.8633 (tp40) cc_final: 0.7876 (tt0) REVERT: H 88 ASN cc_start: 0.8429 (t0) cc_final: 0.7699 (m-40) REVERT: H 104 ASP cc_start: 0.7992 (m-30) cc_final: 0.7612 (m-30) REVERT: C 47 ARG cc_start: 0.7683 (ptp-110) cc_final: 0.7285 (ptp90) REVERT: C 69 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7935 (mm110) REVERT: C 95 SER cc_start: 0.8696 (t) cc_final: 0.8456 (t) outliers start: 14 outliers final: 12 residues processed: 129 average time/residue: 0.1860 time to fit residues: 28.6301 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 : 0.431 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.101699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.077510 restraints weight = 6917.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.079613 restraints weight = 4193.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081064 restraints weight = 3015.373| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.005 0.039 3661 Z= 0.204 Angle : 0.793 8.393 4981 Z= 0.403 Chirality : 0.044 0.148 574 Planarity : 0.005 0.055 641 Dihedral : 5.241 21.200 501 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.02 % Allowed : 27.20 % Favored : 69.77 % 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: -1.71 (0.39), residues: 461 helix: 0.71 (0.70), residues: 49 sheet: -0.18 (0.41), residues: 179 loop : -2.42 (0.37), residues: 233 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 0.011 0.001 PHE L 106 TYR 0.018 0.001 TYR H 53 ARG 0.009 0.001 ARG c 86 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 125) hydrogen bonds : angle 5.22683 ( 336) SS BOND : bond 0.00703 ( 1) SS BOND : angle 1.43826 ( 2) covalent geometry : bond 0.00476 ( 3660) covalent geometry : angle 0.79239 ( 4979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.15 seconds wall clock time: 27 minutes 45.00 seconds (1665.00 seconds total)