Starting phenix.real_space_refine on Fri Dec 27 07:43:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wze_37950/12_2024/8wze_37950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wze_37950/12_2024/8wze_37950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wze_37950/12_2024/8wze_37950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wze_37950/12_2024/8wze_37950.map" model { file = "/net/cci-nas-00/data/ceres_data/8wze_37950/12_2024/8wze_37950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wze_37950/12_2024/8wze_37950.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 18 5.16 5 C 2173 2.51 5 N 557 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3400 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 909 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1661 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Chain breaks: 1 Time building chain proxies: 3.57, per 1000 atoms: 1.05 Number of scatterers: 3400 At special positions: 0 Unit cell: (85.58, 84.024, 66.13, 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 18 16.00 O 652 8.00 N 557 7.00 C 2173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " 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: 0.80 Conformation dependent library (CDL) restraints added in 473.1 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 810 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 23.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 73 through 98 removed outlier: 3.986A pdb=" N MET C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 removed outlier: 4.217A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.579A pdb=" N ILE C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 217 through 241 removed outlier: 4.230A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C 230 " --> pdb=" O MET C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.797A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.668A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.043A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER L 67 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.839A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.249A pdb=" N TRP C 52 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N LEU C 188 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR C 54 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N PHE C 190 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 56 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 192 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR C 58 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP C 194 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU C 60 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 51 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 303 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 351 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: 0.82 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 930 1.33 - 1.45: 588 1.45 - 1.57: 1921 1.57 - 1.69: 1 1.69 - 1.81: 27 Bond restraints: 3467 Sorted by residual: bond pdb=" CG PRO L 40 " pdb=" CD PRO L 40 " ideal model delta sigma weight residual 1.503 1.346 0.157 3.40e-02 8.65e+02 2.13e+01 bond pdb=" CB PRO L 40 " pdb=" CG PRO L 40 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.54e+01 bond pdb=" N LEU C 172 " pdb=" CA LEU C 172 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N PRO L 40 " pdb=" CD PRO L 40 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C LYS C 168 " pdb=" O LYS C 168 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.19e-02 7.06e+03 6.89e+00 ... (remaining 3462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 4673 3.69 - 7.38: 23 7.38 - 11.08: 2 11.08 - 14.77: 1 14.77 - 18.46: 1 Bond angle restraints: 4700 Sorted by residual: angle pdb=" CA PRO L 40 " pdb=" N PRO L 40 " pdb=" CD PRO L 40 " ideal model delta sigma weight residual 112.00 93.54 18.46 1.40e+00 5.10e-01 1.74e+02 angle pdb=" N PRO L 40 " pdb=" CD PRO L 40 " pdb=" CG PRO L 40 " ideal model delta sigma weight residual 103.20 91.67 11.53 1.50e+00 4.44e-01 5.91e+01 angle pdb=" N ASP H 90 " pdb=" CA ASP H 90 " pdb=" C ASP H 90 " ideal model delta sigma weight residual 112.87 104.52 8.35 1.20e+00 6.94e-01 4.85e+01 angle pdb=" CA PRO L 40 " pdb=" CB PRO L 40 " pdb=" CG PRO L 40 " ideal model delta sigma weight residual 104.50 94.57 9.93 1.90e+00 2.77e-01 2.73e+01 angle pdb=" CA THR H 91 " pdb=" C THR H 91 " pdb=" O THR H 91 " ideal model delta sigma weight residual 121.87 116.93 4.94 1.10e+00 8.26e-01 2.01e+01 ... (remaining 4695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 1822 17.74 - 35.48: 207 35.48 - 53.22: 43 53.22 - 70.97: 9 70.97 - 88.71: 4 Dihedral angle restraints: 2085 sinusoidal: 823 harmonic: 1262 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -155.86 69.86 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CA ASN L 50 " pdb=" C ASN L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ILE C 291 " pdb=" C ILE C 291 " pdb=" N ILE C 292 " pdb=" CA ILE C 292 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 2082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 362 0.036 - 0.071: 124 0.071 - 0.107: 37 0.107 - 0.143: 19 0.143 - 0.178: 3 Chirality restraints: 545 Sorted by residual: chirality pdb=" CA PRO L 40 " pdb=" N PRO L 40 " pdb=" C PRO L 40 " pdb=" CB PRO L 40 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA LEU C 172 " pdb=" N LEU C 172 " pdb=" C LEU C 172 " pdb=" CB LEU C 172 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB THR L 74 " pdb=" CA THR L 74 " pdb=" OG1 THR L 74 " pdb=" CG2 THR L 74 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 542 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " -0.100 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO L 40 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 172 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LEU C 172 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU C 172 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 173 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO L 40 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C PRO L 40 " 0.032 2.00e-02 2.50e+03 pdb=" O PRO L 40 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY L 41 " -0.011 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 176 2.73 - 3.27: 3158 3.27 - 3.81: 5213 3.81 - 4.36: 6469 4.36 - 4.90: 11244 Nonbonded interactions: 26260 Sorted by model distance: nonbonded pdb=" OG1 THR C 253 " pdb=" OE2 GLU C 256 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR H 99 " pdb=" OH TYR L 96 " model vdw 2.216 3.040 nonbonded pdb=" OG SER L 25 " pdb=" O GLY L 27 " model vdw 2.269 3.040 nonbonded pdb=" O TYR H 32 " pdb=" OG1 THR H 53 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLN C 284 " pdb=" OH TYR C 306 " model vdw 2.319 3.040 ... (remaining 26255 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 0.196 3467 Z= 0.298 Angle : 0.753 18.462 4700 Z= 0.466 Chirality : 0.045 0.178 545 Planarity : 0.007 0.135 586 Dihedral : 15.536 88.707 1263 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.98 % Favored : 95.78 % Rotamer: Outliers : 0.78 % Allowed : 19.17 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.41), residues: 427 helix: -1.51 (0.45), residues: 114 sheet: -0.99 (0.44), residues: 154 loop : -1.90 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS L 30 PHE 0.016 0.001 PHE L 46 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: C 216 ASN cc_start: 0.5312 (t0) cc_final: 0.5037 (p0) REVERT: C 226 MET cc_start: 0.8130 (ttm) cc_final: 0.7920 (ptp) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.1596 time to fit residues: 15.8691 Evaluate side-chains 69 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN C 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3467 Z= 0.253 Angle : 0.542 6.314 4700 Z= 0.286 Chirality : 0.044 0.149 545 Planarity : 0.004 0.031 586 Dihedral : 5.312 31.851 466 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.92 % Allowed : 17.62 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.89 (0.41), residues: 427 helix: -0.65 (0.48), residues: 117 sheet: -0.92 (0.44), residues: 155 loop : -1.88 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.002 PHE L 91 TYR 0.020 0.002 TYR L 49 ARG 0.002 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: C 201 ASN cc_start: 0.7492 (t0) cc_final: 0.7186 (t0) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 0.1337 time to fit residues: 14.0063 Evaluate side-chains 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3467 Z= 0.228 Angle : 0.530 6.845 4700 Z= 0.275 Chirality : 0.044 0.143 545 Planarity : 0.004 0.037 586 Dihedral : 5.263 31.493 466 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.66 % Allowed : 18.65 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.41), residues: 427 helix: -0.13 (0.50), residues: 114 sheet: -0.88 (0.44), residues: 156 loop : -1.90 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE H 70 TYR 0.015 0.001 TYR L 49 ARG 0.001 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.504 Fit side-chains REVERT: H 38 LYS cc_start: 0.8051 (tttt) cc_final: 0.6898 (tptp) REVERT: C 201 ASN cc_start: 0.7461 (t0) cc_final: 0.7117 (t0) outliers start: 18 outliers final: 13 residues processed: 81 average time/residue: 0.1482 time to fit residues: 15.1773 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 40 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3467 Z= 0.203 Angle : 0.502 5.788 4700 Z= 0.261 Chirality : 0.043 0.147 545 Planarity : 0.003 0.031 586 Dihedral : 4.877 30.083 464 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.92 % Allowed : 18.65 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.54 (0.41), residues: 427 helix: 0.02 (0.50), residues: 113 sheet: -0.86 (0.44), residues: 156 loop : -1.82 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.001 PHE H 70 TYR 0.016 0.001 TYR L 49 ARG 0.001 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.391 Fit side-chains REVERT: H 38 LYS cc_start: 0.7986 (tttt) cc_final: 0.6947 (tptp) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.1425 time to fit residues: 15.4091 Evaluate side-chains 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3467 Z= 0.264 Angle : 0.529 5.667 4700 Z= 0.274 Chirality : 0.044 0.151 545 Planarity : 0.003 0.028 586 Dihedral : 5.033 34.452 464 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.70 % Allowed : 20.98 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.62 (0.41), residues: 427 helix: 0.05 (0.50), residues: 113 sheet: -0.93 (0.43), residues: 158 loop : -1.93 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.002 PHE L 91 TYR 0.015 0.002 TYR L 49 ARG 0.001 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.369 Fit side-chains REVERT: H 38 LYS cc_start: 0.7966 (tttt) cc_final: 0.6912 (tptp) outliers start: 22 outliers final: 15 residues processed: 79 average time/residue: 0.1379 time to fit residues: 13.7679 Evaluate side-chains 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3467 Z= 0.254 Angle : 0.529 5.426 4700 Z= 0.272 Chirality : 0.044 0.171 545 Planarity : 0.003 0.027 586 Dihedral : 5.043 35.026 464 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.44 % Allowed : 20.47 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.56 (0.41), residues: 427 helix: 0.14 (0.50), residues: 113 sheet: -0.97 (0.43), residues: 159 loop : -1.84 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.002 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.001 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.398 Fit side-chains REVERT: H 38 LYS cc_start: 0.7964 (tttt) cc_final: 0.6927 (tptp) outliers start: 21 outliers final: 17 residues processed: 79 average time/residue: 0.1443 time to fit residues: 14.5241 Evaluate side-chains 81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3467 Z= 0.234 Angle : 0.510 5.499 4700 Z= 0.264 Chirality : 0.044 0.170 545 Planarity : 0.003 0.029 586 Dihedral : 4.948 34.224 464 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.18 % Allowed : 20.47 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.51 (0.41), residues: 427 helix: 0.22 (0.50), residues: 113 sheet: -0.89 (0.43), residues: 158 loop : -1.90 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE L 91 TYR 0.013 0.001 TYR L 49 ARG 0.001 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.392 Fit side-chains REVERT: H 38 LYS cc_start: 0.7931 (tttt) cc_final: 0.6909 (tptp) REVERT: H 87 LYS cc_start: 0.6148 (mtmt) cc_final: 0.5300 (mmmt) REVERT: L 49 TYR cc_start: 0.8643 (m-80) cc_final: 0.8362 (m-80) REVERT: C 222 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: C 268 ASN cc_start: 0.7848 (m-40) cc_final: 0.7348 (t0) outliers start: 20 outliers final: 17 residues processed: 77 average time/residue: 0.1379 time to fit residues: 13.4738 Evaluate side-chains 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3467 Z= 0.182 Angle : 0.481 5.363 4700 Z= 0.250 Chirality : 0.043 0.170 545 Planarity : 0.003 0.027 586 Dihedral : 4.778 30.658 464 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.92 % Allowed : 20.73 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.32 (0.42), residues: 427 helix: 0.57 (0.52), residues: 110 sheet: -0.86 (0.43), residues: 158 loop : -1.81 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE H 70 TYR 0.012 0.001 TYR L 49 ARG 0.001 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.403 Fit side-chains REVERT: H 38 LYS cc_start: 0.7878 (tttt) cc_final: 0.6858 (tptp) REVERT: H 87 LYS cc_start: 0.6140 (mtmt) cc_final: 0.5289 (mmmt) REVERT: L 78 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.5054 (tt) REVERT: C 268 ASN cc_start: 0.7822 (m-40) cc_final: 0.7323 (t0) REVERT: C 289 MET cc_start: 0.7065 (tpt) cc_final: 0.6601 (tpt) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1619 time to fit residues: 16.5389 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3467 Z= 0.230 Angle : 0.519 5.350 4700 Z= 0.267 Chirality : 0.044 0.175 545 Planarity : 0.003 0.028 586 Dihedral : 4.881 33.396 464 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.92 % Allowed : 20.21 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.30 (0.42), residues: 427 helix: 0.55 (0.51), residues: 110 sheet: -0.81 (0.43), residues: 156 loop : -1.80 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE L 91 TYR 0.017 0.002 TYR L 49 ARG 0.001 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.394 Fit side-chains REVERT: H 38 LYS cc_start: 0.7842 (tttt) cc_final: 0.6816 (tptp) REVERT: H 87 LYS cc_start: 0.6105 (mtmt) cc_final: 0.5297 (mmmt) REVERT: L 78 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.5050 (tt) REVERT: C 222 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: C 268 ASN cc_start: 0.7795 (m-40) cc_final: 0.7310 (t0) outliers start: 19 outliers final: 13 residues processed: 77 average time/residue: 0.1542 time to fit residues: 14.9199 Evaluate side-chains 81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3467 Z= 0.181 Angle : 0.492 5.358 4700 Z= 0.254 Chirality : 0.043 0.191 545 Planarity : 0.003 0.029 586 Dihedral : 4.712 30.090 464 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.89 % Allowed : 21.50 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.23 (0.42), residues: 427 helix: 0.66 (0.52), residues: 110 sheet: -0.84 (0.43), residues: 156 loop : -1.73 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE L 91 TYR 0.019 0.001 TYR L 49 ARG 0.001 0.000 ARG C 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.404 Fit side-chains REVERT: H 38 LYS cc_start: 0.7852 (tttt) cc_final: 0.6824 (tptp) REVERT: H 87 LYS cc_start: 0.6125 (mtmt) cc_final: 0.5338 (mmmt) REVERT: L 78 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5045 (tt) REVERT: C 268 ASN cc_start: 0.7748 (m-40) cc_final: 0.7283 (t0) REVERT: C 289 MET cc_start: 0.7058 (tpt) cc_final: 0.6600 (tpt) outliers start: 15 outliers final: 12 residues processed: 76 average time/residue: 0.1462 time to fit residues: 14.0141 Evaluate side-chains 79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.181032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154495 restraints weight = 4105.930| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.06 r_work: 0.3460 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3467 Z= 0.143 Angle : 0.474 5.302 4700 Z= 0.244 Chirality : 0.043 0.192 545 Planarity : 0.003 0.032 586 Dihedral : 4.439 24.796 464 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.11 % Allowed : 22.02 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.04 (0.42), residues: 427 helix: 0.88 (0.53), residues: 109 sheet: -0.77 (0.43), residues: 155 loop : -1.58 (0.48), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 PHE 0.016 0.001 PHE L 46 TYR 0.017 0.001 TYR L 49 ARG 0.001 0.000 ARG C 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.48 seconds wall clock time: 26 minutes 3.07 seconds (1563.07 seconds total)