Starting phenix.real_space_refine on Fri Aug 22 13:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5f_37290/08_2025/8w5f_37290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5f_37290/08_2025/8w5f_37290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5f_37290/08_2025/8w5f_37290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5f_37290/08_2025/8w5f_37290.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5f_37290/08_2025/8w5f_37290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5f_37290/08_2025/8w5f_37290.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.194 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 10 5.16 5 C 2326 2.51 5 N 637 2.21 5 O 727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3700 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 790 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "c" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 1.10, per 1000 atoms: 0.30 Number of scatterers: 3700 At special positions: 0 Unit cell: (88.4, 66.64, 81.6, 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 10 16.00 O 727 8.00 N 637 7.00 C 2326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " 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: 0.25 Conformation dependent library (CDL) restraints added in 102.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 10.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'c' and resid 101 through 116 removed outlier: 3.645A pdb=" N ARG c 109 " --> pdb=" O ARG c 105 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR c 110 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 127 removed outlier: 3.630A pdb=" N GLN c 127 " --> pdb=" O ASP c 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 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 removed outlier: 4.037A pdb=" N ASP C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.514A pdb=" N VAL L 37 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR L 89 " --> pdb=" O CYS L 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.837A pdb=" N GLU H 29 " --> pdb=" O THR H 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.542A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 6 through 11 removed outlier: 6.180A pdb=" N GLN c 17 " --> pdb=" O ASN c 10 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLN c 87 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR C 97 " --> pdb=" O GLN c 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP c 91 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 62 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 47 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 327 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: 0.52 Time building geometry restraints manager: 0.34 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: 1211 1.34 - 1.46: 773 1.46 - 1.58: 1779 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3775 Sorted by residual: bond pdb=" C SER L 25 " pdb=" N PRO L 26 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" CB PRO c 28 " pdb=" CG PRO c 28 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.34e+00 bond pdb=" CA GLU H 108 " pdb=" CB GLU H 108 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.30e-02 5.92e+03 8.58e-01 bond pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.41e-02 5.03e+03 8.39e-01 bond pdb=" N PRO H 26 " pdb=" CA PRO H 26 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.11e-01 ... (remaining 3770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 5054 2.77 - 5.55: 73 5.55 - 8.32: 9 8.32 - 11.09: 1 11.09 - 13.86: 1 Bond angle restraints: 5138 Sorted by residual: angle pdb=" C VAL H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta sigma weight residual 121.80 135.66 -13.86 2.44e+00 1.68e-01 3.23e+01 angle pdb=" C SER L 30 " pdb=" N VAL L 31 " pdb=" CA VAL L 31 " ideal model delta sigma weight residual 121.97 128.98 -7.01 1.80e+00 3.09e-01 1.52e+01 angle pdb=" C SER L 98 " pdb=" N GLU L 99 " pdb=" CA GLU L 99 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" N PRO H 26 " pdb=" CA PRO H 26 " pdb=" C PRO H 26 " ideal model delta sigma weight residual 112.47 120.34 -7.87 2.06e+00 2.36e-01 1.46e+01 angle pdb=" C GLY c 12 " pdb=" N LYS c 13 " pdb=" CA LYS c 13 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 5133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 1998 15.75 - 31.50: 216 31.50 - 47.25: 35 47.25 - 63.00: 8 63.00 - 78.75: 3 Dihedral angle restraints: 2260 sinusoidal: 858 harmonic: 1402 Sorted by residual: dihedral pdb=" CA SER L 25 " pdb=" C SER L 25 " pdb=" N PRO L 26 " pdb=" CA PRO L 26 " ideal model delta harmonic sigma weight residual -180.00 -137.47 -42.53 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA ILE c 11 " pdb=" C ILE c 11 " pdb=" N GLY c 12 " pdb=" CA GLY c 12 " ideal model delta harmonic sigma weight residual 180.00 -138.43 -41.57 0 5.00e+00 4.00e-02 6.91e+01 dihedral pdb=" CA TRP L 114 " pdb=" C TRP L 114 " pdb=" N THR L 115 " pdb=" CA THR L 115 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 2257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 454 0.052 - 0.103: 102 0.103 - 0.154: 30 0.154 - 0.206: 1 0.206 - 0.257: 1 Chirality restraints: 588 Sorted by residual: chirality pdb=" CA PRO H 26 " pdb=" N PRO H 26 " pdb=" C PRO H 26 " pdb=" CB PRO H 26 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASN H 74 " pdb=" N ASN H 74 " pdb=" C ASN H 74 " pdb=" CB ASN H 74 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA THR L 112 " pdb=" N THR L 112 " pdb=" C THR L 112 " pdb=" CB THR L 112 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 585 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 25 " 0.065 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO H 26 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO H 26 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO H 26 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 25 " -0.059 5.00e-02 4.00e+02 9.03e-02 1.30e+01 pdb=" N PRO L 26 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO L 26 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 26 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 25 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C GLN H 25 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN H 25 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO H 26 " 0.013 2.00e-02 2.50e+03 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1130 2.82 - 3.34: 3163 3.34 - 3.86: 5529 3.86 - 4.38: 6386 4.38 - 4.90: 11858 Nonbonded interactions: 28066 Sorted by model distance: nonbonded pdb=" NZ LYS H 86 " pdb=" O SER H 104 " model vdw 2.296 3.120 nonbonded pdb=" NH1 ARG L 79 " pdb=" OD2 ASP L 100 " model vdw 2.303 3.120 nonbonded pdb=" N THR H 106 " pdb=" OD2 ASP H 109 " model vdw 2.333 3.120 nonbonded pdb=" O ASN C 70 " pdb=" ND2 ASN C 70 " model vdw 2.335 3.120 nonbonded pdb=" OE2 GLU H 65 " pdb=" NZ LYS H 82 " model vdw 2.371 3.120 ... (remaining 28061 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.250 Find NCS groups from input model: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.004 0.058 3777 Z= 0.169 Angle : 0.822 13.864 5142 Z= 0.433 Chirality : 0.048 0.257 588 Planarity : 0.007 0.100 665 Dihedral : 13.392 78.749 1356 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.47 % Allowed : 9.85 % Favored : 88.68 % Rotamer: Outliers : 0.25 % Allowed : 0.49 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.36), residues: 477 helix: -1.02 (0.75), residues: 44 sheet: -1.42 (0.38), residues: 190 loop : -2.68 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 117 TYR 0.012 0.001 TYR L 54 PHE 0.008 0.001 PHE L 116 TRP 0.017 0.002 TRP H 132 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3775) covalent geometry : angle 0.82229 ( 5138) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.65307 ( 4) hydrogen bonds : bond 0.18694 ( 123) hydrogen bonds : angle 8.03197 ( 327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.085 Fit side-chains REVERT: L 54 TYR cc_start: 0.9216 (m-80) cc_final: 0.8931 (m-80) REVERT: C 27 ASN cc_start: 0.8485 (t0) cc_final: 0.8012 (t0) REVERT: C 30 ASN cc_start: 0.9021 (p0) cc_final: 0.8619 (p0) REVERT: C 60 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8020 (pttp) outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.0715 time to fit residues: 7.9469 Evaluate side-chains 93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.093252 restraints weight = 5059.416| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.33 r_work: 0.2970 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3777 Z= 0.187 Angle : 0.799 11.333 5142 Z= 0.411 Chirality : 0.049 0.240 588 Planarity : 0.007 0.087 665 Dihedral : 6.183 40.637 525 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 1.47 % Allowed : 10.69 % Favored : 87.84 % Rotamer: Outliers : 0.99 % Allowed : 11.85 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.37), residues: 477 helix: -0.41 (0.76), residues: 46 sheet: -1.01 (0.39), residues: 187 loop : -2.59 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 117 TYR 0.011 0.002 TYR L 54 PHE 0.008 0.001 PHE L 116 TRP 0.014 0.002 TRP H 132 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3775) covalent geometry : angle 0.79930 ( 5138) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.93023 ( 4) hydrogen bonds : bond 0.04675 ( 123) hydrogen bonds : angle 5.53322 ( 327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.122 Fit side-chains REVERT: L 92 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8600 (ttpt) REVERT: H 65 GLU cc_start: 0.8992 (tp30) cc_final: 0.8778 (tp30) REVERT: H 109 ASP cc_start: 0.7932 (m-30) cc_final: 0.7605 (m-30) REVERT: c 127 GLN cc_start: 0.8911 (mp10) cc_final: 0.8447 (mp10) REVERT: C 27 ASN cc_start: 0.8762 (t0) cc_final: 0.8291 (t0) REVERT: C 30 ASN cc_start: 0.9132 (p0) cc_final: 0.8657 (p0) REVERT: C 60 LYS cc_start: 0.8881 (mtmt) cc_final: 0.7556 (pttp) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.0621 time to fit residues: 8.0218 Evaluate side-chains 102 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093720 restraints weight = 5014.475| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.28 r_work: 0.2942 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3777 Z= 0.218 Angle : 0.804 9.877 5142 Z= 0.415 Chirality : 0.050 0.238 588 Planarity : 0.006 0.084 665 Dihedral : 6.035 41.314 523 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 1.47 % Allowed : 10.90 % Favored : 87.63 % Rotamer: Outliers : 2.72 % Allowed : 14.57 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.37), residues: 477 helix: -0.31 (0.79), residues: 48 sheet: -0.90 (0.39), residues: 187 loop : -2.57 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 117 TYR 0.011 0.002 TYR L 67 PHE 0.010 0.002 PHE L 91 TRP 0.013 0.002 TRP H 132 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 3775) covalent geometry : angle 0.80391 ( 5138) SS BOND : bond 0.00313 ( 2) SS BOND : angle 0.93032 ( 4) hydrogen bonds : bond 0.04717 ( 123) hydrogen bonds : angle 5.33643 ( 327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.126 Fit side-chains REVERT: L 92 LYS cc_start: 0.9125 (ptmm) cc_final: 0.8627 (ttpt) REVERT: H 109 ASP cc_start: 0.7958 (m-30) cc_final: 0.7559 (m-30) REVERT: c 126 ASP cc_start: 0.8895 (m-30) cc_final: 0.8685 (m-30) REVERT: c 127 GLN cc_start: 0.8989 (mp10) cc_final: 0.8554 (mp10) REVERT: C 27 ASN cc_start: 0.8759 (t0) cc_final: 0.8299 (t0) REVERT: C 30 ASN cc_start: 0.9141 (p0) cc_final: 0.8675 (p0) REVERT: C 45 GLU cc_start: 0.8665 (pt0) cc_final: 0.8449 (pt0) REVERT: C 60 LYS cc_start: 0.8811 (mtmt) cc_final: 0.7937 (pttp) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.0612 time to fit residues: 7.7831 Evaluate side-chains 104 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 87 GLN C 69 GLN ** C 70 ASN ** 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 = 0.3456 r_free = 0.3456 target = 0.123472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.096873 restraints weight = 5001.919| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.28 r_work: 0.2981 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3777 Z= 0.141 Angle : 0.736 10.639 5142 Z= 0.374 Chirality : 0.047 0.277 588 Planarity : 0.007 0.120 665 Dihedral : 5.630 35.576 523 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 1.26 % Allowed : 9.64 % Favored : 89.10 % Rotamer: Outliers : 2.72 % Allowed : 16.30 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.37), residues: 477 helix: -0.04 (0.78), residues: 46 sheet: -0.78 (0.39), residues: 187 loop : -2.51 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.011 0.001 TYR L 48 PHE 0.007 0.001 PHE L 80 TRP 0.013 0.001 TRP H 66 HIS 0.001 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3775) covalent geometry : angle 0.73612 ( 5138) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.66484 ( 4) hydrogen bonds : bond 0.03733 ( 123) hydrogen bonds : angle 5.04967 ( 327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.132 Fit side-chains REVERT: L 92 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8550 (ttpt) REVERT: H 109 ASP cc_start: 0.7903 (m-30) cc_final: 0.7505 (m-30) REVERT: c 63 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8568 (mtpp) REVERT: C 13 LYS cc_start: 0.8813 (tptt) cc_final: 0.8517 (tppt) REVERT: C 27 ASN cc_start: 0.8718 (t0) cc_final: 0.8294 (t0) REVERT: C 30 ASN cc_start: 0.9094 (p0) cc_final: 0.8707 (p0) REVERT: C 45 GLU cc_start: 0.8661 (pt0) cc_final: 0.8419 (pt0) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.0654 time to fit residues: 8.6202 Evaluate side-chains 108 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092366 restraints weight = 5124.221| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.27 r_work: 0.2925 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3777 Z= 0.251 Angle : 0.821 9.787 5142 Z= 0.423 Chirality : 0.051 0.250 588 Planarity : 0.007 0.098 665 Dihedral : 6.089 41.081 523 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.00 % Favored : 85.95 % Rotamer: Outliers : 3.21 % Allowed : 17.04 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.38), residues: 477 helix: -0.11 (0.78), residues: 46 sheet: -0.88 (0.39), residues: 188 loop : -2.52 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 117 TYR 0.013 0.002 TYR c 89 PHE 0.011 0.002 PHE c 94 TRP 0.011 0.002 TRP H 132 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 3775) covalent geometry : angle 0.82048 ( 5138) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.93047 ( 4) hydrogen bonds : bond 0.04682 ( 123) hydrogen bonds : angle 5.22534 ( 327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.119 Fit side-chains REVERT: L 92 LYS cc_start: 0.9136 (ptmm) cc_final: 0.8663 (ttpt) REVERT: L 97 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: H 109 ASP cc_start: 0.8021 (m-30) cc_final: 0.7585 (m-30) REVERT: c 127 GLN cc_start: 0.9022 (mp10) cc_final: 0.8588 (mp10) REVERT: C 13 LYS cc_start: 0.8771 (tptt) cc_final: 0.8509 (tppt) REVERT: C 27 ASN cc_start: 0.8741 (t0) cc_final: 0.8432 (t0) REVERT: C 45 GLU cc_start: 0.8708 (pt0) cc_final: 0.8443 (pt0) outliers start: 13 outliers final: 9 residues processed: 102 average time/residue: 0.0630 time to fit residues: 7.8635 Evaluate side-chains 107 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.094134 restraints weight = 5039.351| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.26 r_work: 0.2953 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3777 Z= 0.183 Angle : 0.758 8.911 5142 Z= 0.392 Chirality : 0.049 0.249 588 Planarity : 0.006 0.086 665 Dihedral : 5.841 37.417 523 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.32 % Favored : 87.63 % Rotamer: Outliers : 4.69 % Allowed : 17.53 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.37), residues: 477 helix: -0.09 (0.78), residues: 46 sheet: -0.77 (0.39), residues: 187 loop : -2.53 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 117 TYR 0.011 0.002 TYR L 67 PHE 0.010 0.001 PHE c 94 TRP 0.013 0.002 TRP H 66 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3775) covalent geometry : angle 0.75776 ( 5138) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.81809 ( 4) hydrogen bonds : bond 0.04077 ( 123) hydrogen bonds : angle 5.07742 ( 327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.092 Fit side-chains REVERT: L 92 LYS cc_start: 0.9117 (ptmm) cc_final: 0.8646 (ttpt) REVERT: L 97 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: H 86 LYS cc_start: 0.8995 (tppp) cc_final: 0.8696 (tptm) REVERT: H 109 ASP cc_start: 0.7947 (m-30) cc_final: 0.7561 (m-30) REVERT: c 59 ARG cc_start: 0.7276 (mtp85) cc_final: 0.6751 (mtp85) REVERT: c 127 GLN cc_start: 0.9018 (mp10) cc_final: 0.8565 (mp10) REVERT: C 13 LYS cc_start: 0.8813 (tptt) cc_final: 0.8554 (tppt) REVERT: C 27 ASN cc_start: 0.8723 (t0) cc_final: 0.8425 (t0) REVERT: C 45 GLU cc_start: 0.8677 (pt0) cc_final: 0.8440 (pt0) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.0737 time to fit residues: 9.9319 Evaluate side-chains 119 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095498 restraints weight = 5097.950| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.30 r_work: 0.2972 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3777 Z= 0.149 Angle : 0.733 8.493 5142 Z= 0.379 Chirality : 0.047 0.246 588 Planarity : 0.006 0.080 665 Dihedral : 5.673 36.616 523 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.05 % Allowed : 10.90 % Favored : 88.05 % Rotamer: Outliers : 4.44 % Allowed : 20.25 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.38), residues: 477 helix: -0.05 (0.78), residues: 46 sheet: -0.68 (0.39), residues: 187 loop : -2.49 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.010 0.001 TYR L 48 PHE 0.008 0.001 PHE c 94 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3775) covalent geometry : angle 0.73332 ( 5138) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.66970 ( 4) hydrogen bonds : bond 0.03715 ( 123) hydrogen bonds : angle 4.93651 ( 327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.151 Fit side-chains REVERT: L 92 LYS cc_start: 0.9086 (ptmm) cc_final: 0.8603 (ttpt) REVERT: L 97 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: H 86 LYS cc_start: 0.8988 (tppp) cc_final: 0.8688 (tptm) REVERT: H 109 ASP cc_start: 0.7949 (m-30) cc_final: 0.7528 (m-30) REVERT: c 59 ARG cc_start: 0.7252 (mtp85) cc_final: 0.6709 (mtp85) REVERT: C 13 LYS cc_start: 0.8828 (tptt) cc_final: 0.8560 (tppt) REVERT: C 27 ASN cc_start: 0.8696 (t0) cc_final: 0.8303 (t0) REVERT: C 30 ASN cc_start: 0.9067 (p0) cc_final: 0.8704 (p0) REVERT: C 45 GLU cc_start: 0.8653 (pt0) cc_final: 0.8418 (pt0) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.0718 time to fit residues: 9.4707 Evaluate side-chains 113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093613 restraints weight = 5062.366| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.28 r_work: 0.2944 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3777 Z= 0.203 Angle : 0.774 8.223 5142 Z= 0.402 Chirality : 0.049 0.242 588 Planarity : 0.006 0.077 665 Dihedral : 5.822 39.786 523 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.95 % Favored : 87.00 % Rotamer: Outliers : 4.44 % Allowed : 20.49 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.38), residues: 477 helix: -0.02 (0.79), residues: 46 sheet: -0.65 (0.39), residues: 187 loop : -2.47 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 117 TYR 0.011 0.002 TYR L 67 PHE 0.011 0.002 PHE c 94 TRP 0.012 0.002 TRP H 66 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3775) covalent geometry : angle 0.77403 ( 5138) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.81693 ( 4) hydrogen bonds : bond 0.04200 ( 123) hydrogen bonds : angle 5.07060 ( 327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.140 Fit side-chains REVERT: L 92 LYS cc_start: 0.9111 (ptmm) cc_final: 0.8633 (ttpt) REVERT: L 97 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: H 86 LYS cc_start: 0.8977 (tppp) cc_final: 0.8625 (tptm) REVERT: H 109 ASP cc_start: 0.7987 (m-30) cc_final: 0.7633 (m-30) REVERT: c 59 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6597 (mmm160) REVERT: c 127 GLN cc_start: 0.9048 (mp10) cc_final: 0.8592 (mp10) REVERT: C 13 LYS cc_start: 0.8885 (tptt) cc_final: 0.8635 (tppt) REVERT: C 27 ASN cc_start: 0.8699 (t0) cc_final: 0.8396 (t0) REVERT: C 45 GLU cc_start: 0.8686 (pt0) cc_final: 0.8424 (pt0) outliers start: 18 outliers final: 16 residues processed: 108 average time/residue: 0.0743 time to fit residues: 9.6762 Evaluate side-chains 115 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095599 restraints weight = 5003.441| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.29 r_work: 0.2976 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3777 Z= 0.155 Angle : 0.737 8.160 5142 Z= 0.382 Chirality : 0.048 0.245 588 Planarity : 0.005 0.072 665 Dihedral : 5.653 37.534 523 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.27 % Favored : 88.89 % Rotamer: Outliers : 4.44 % Allowed : 20.00 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.38), residues: 477 helix: 0.09 (0.79), residues: 46 sheet: -0.59 (0.39), residues: 187 loop : -2.42 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.010 0.001 TYR L 48 PHE 0.008 0.001 PHE c 94 TRP 0.013 0.001 TRP H 132 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3775) covalent geometry : angle 0.73676 ( 5138) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.69667 ( 4) hydrogen bonds : bond 0.03753 ( 123) hydrogen bonds : angle 4.92089 ( 327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.140 Fit side-chains REVERT: L 88 GLN cc_start: 0.8490 (tt0) cc_final: 0.8278 (mt0) REVERT: L 92 LYS cc_start: 0.9088 (ptmm) cc_final: 0.8613 (ttpt) REVERT: L 97 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: H 86 LYS cc_start: 0.8975 (tppp) cc_final: 0.8651 (tptm) REVERT: H 109 ASP cc_start: 0.7935 (m-30) cc_final: 0.7564 (m-30) REVERT: c 127 GLN cc_start: 0.9035 (mp10) cc_final: 0.8573 (mp10) REVERT: C 13 LYS cc_start: 0.8891 (tptt) cc_final: 0.8650 (tppt) REVERT: C 27 ASN cc_start: 0.8680 (t0) cc_final: 0.8283 (t0) REVERT: C 30 ASN cc_start: 0.9061 (p0) cc_final: 0.8691 (p0) REVERT: C 45 GLU cc_start: 0.8670 (pt0) cc_final: 0.8418 (pt0) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.0702 time to fit residues: 9.3859 Evaluate side-chains 117 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095001 restraints weight = 5151.402| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.30 r_work: 0.2964 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3777 Z= 0.167 Angle : 0.743 8.136 5142 Z= 0.386 Chirality : 0.048 0.243 588 Planarity : 0.005 0.069 665 Dihedral : 5.629 37.488 523 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.74 % Favored : 87.42 % Rotamer: Outliers : 4.20 % Allowed : 20.49 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.38), residues: 477 helix: 0.10 (0.79), residues: 46 sheet: -0.60 (0.39), residues: 187 loop : -2.41 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.010 0.001 TYR c 89 PHE 0.009 0.001 PHE c 94 TRP 0.013 0.001 TRP H 132 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3775) covalent geometry : angle 0.74299 ( 5138) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.70635 ( 4) hydrogen bonds : bond 0.03851 ( 123) hydrogen bonds : angle 4.95972 ( 327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.144 Fit side-chains REVERT: L 88 GLN cc_start: 0.8502 (tt0) cc_final: 0.8295 (mt0) REVERT: L 92 LYS cc_start: 0.9087 (ptmm) cc_final: 0.8606 (ttpt) REVERT: L 97 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: H 86 LYS cc_start: 0.8979 (tppp) cc_final: 0.8654 (tptm) REVERT: H 109 ASP cc_start: 0.7984 (m-30) cc_final: 0.7613 (m-30) REVERT: c 127 GLN cc_start: 0.9053 (mp10) cc_final: 0.8602 (mp10) REVERT: C 13 LYS cc_start: 0.8889 (tptt) cc_final: 0.8630 (tppt) REVERT: C 27 ASN cc_start: 0.8671 (t0) cc_final: 0.8366 (t0) REVERT: C 45 GLU cc_start: 0.8678 (pt0) cc_final: 0.8441 (pt0) outliers start: 17 outliers final: 16 residues processed: 105 average time/residue: 0.0729 time to fit residues: 9.3499 Evaluate side-chains 115 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095510 restraints weight = 4961.240| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.25 r_work: 0.2976 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3777 Z= 0.165 Angle : 0.741 8.148 5142 Z= 0.384 Chirality : 0.048 0.242 588 Planarity : 0.005 0.066 665 Dihedral : 5.603 37.275 523 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.90 % Favored : 88.26 % Rotamer: Outliers : 3.95 % Allowed : 20.74 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.38), residues: 477 helix: 0.10 (0.79), residues: 46 sheet: -0.59 (0.39), residues: 187 loop : -2.40 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.010 0.001 TYR c 89 PHE 0.010 0.001 PHE c 94 TRP 0.013 0.001 TRP H 132 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3775) covalent geometry : angle 0.74137 ( 5138) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.69666 ( 4) hydrogen bonds : bond 0.03830 ( 123) hydrogen bonds : angle 4.92308 ( 327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.74 seconds wall clock time: 18 minutes 44.46 seconds (1124.46 seconds total)