Starting phenix.real_space_refine on Fri May 9 18:41:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wze_37950/05_2025/8wze_37950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wze_37950/05_2025/8wze_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_37950/05_2025/8wze_37950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wze_37950/05_2025/8wze_37950.map" model { file = "/net/cci-nas-00/data/ceres_data/8wze_37950/05_2025/8wze_37950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wze_37950/05_2025/8wze_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-5687/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: 3.07, per 1000 atoms: 0.90 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: 0.72 Conformation dependent library (CDL) restraints added in 387.2 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: 0.38 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: 0.80 Time building geometry restraints manager: 0.87 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- 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 3471 Z= 0.231 Angle : 0.753 18.462 4708 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 Details of bonding type rmsd hydrogen bonds : bond 0.25549 ( 121) hydrogen bonds : angle 9.23339 ( 351) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.44946 ( 8) covalent geometry : bond 0.00545 ( 3467) covalent geometry : angle 0.75298 ( 4700) *********************** 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 : 0.400 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: 0.1406 time to fit residues: 13.9719 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 : 0.398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.172421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144527 restraints weight = 4032.729| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.12 r_work: 0.3390 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 3471 Z= 0.161 Angle : 0.542 6.314 4708 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 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 121) hydrogen bonds : angle 5.60704 ( 351) SS BOND : bond 0.00191 ( 4) SS BOND : angle 0.58778 ( 8) covalent geometry : bond 0.00395 ( 3467) covalent geometry : angle 0.54184 ( 4700) *********************** 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 : 0.370 Fit side-chains revert: symmetry clash REVERT: C 201 ASN cc_start: 0.8057 (t0) cc_final: 0.7778 (t0) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 0.1355 time to fit residues: 14.2210 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 : 0.469 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132805 restraints weight = 4134.057| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.98 r_work: 0.3431 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 0.026 3471 Z= 0.142 Angle : 0.530 6.955 4708 Z= 0.275 Chirality : 0.044 0.143 545 Planarity : 0.004 0.038 586 Dihedral : 5.252 31.229 466 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.87 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: -0.12 (0.50), residues: 114 sheet: -0.88 (0.44), residues: 156 loop : -1.91 (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 235 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 121) hydrogen bonds : angle 5.25781 ( 351) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.05255 ( 8) covalent geometry : bond 0.00343 ( 3467) covalent geometry : angle 0.52852 ( 4700) *********************** 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 : 0.415 Fit side-chains REVERT: H 38 LYS cc_start: 0.8357 (tttt) cc_final: 0.7765 (tptp) REVERT: C 201 ASN cc_start: 0.8003 (t0) cc_final: 0.7669 (t0) outliers start: 18 outliers final: 13 residues processed: 81 average time/residue: 0.1360 time to fit residues: 13.8556 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 : 0.408 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 0.0070 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.177366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150377 restraints weight = 4120.817| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.09 r_work: 0.3433 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3471 Z= 0.118 Angle : 0.491 5.794 4708 Z= 0.255 Chirality : 0.043 0.146 545 Planarity : 0.003 0.030 586 Dihedral : 4.785 28.324 464 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.40 % Allowed : 19.17 % 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: -1.52 (0.41), residues: 427 helix: 0.06 (0.50), residues: 113 sheet: -0.84 (0.44), residues: 156 loop : -1.83 (0.47), residues: 158 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 0.013 0.001 PHE H 70 TYR 0.015 0.001 TYR L 49 ARG 0.002 0.000 ARG C 235 Details of bonding type rmsd hydrogen bonds : bond 0.02766 ( 121) hydrogen bonds : angle 4.91962 ( 351) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.59711 ( 8) covalent geometry : bond 0.00285 ( 3467) covalent geometry : angle 0.49086 ( 4700) *********************** 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 88 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.408 Fit side-chains REVERT: H 38 LYS cc_start: 0.8282 (tttt) cc_final: 0.7799 (tptp) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.1375 time to fit residues: 14.4471 Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 159 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 290 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.174463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147166 restraints weight = 4223.546| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.14 r_work: 0.3361 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3471 Z= 0.178 Angle : 0.543 5.538 4708 Z= 0.281 Chirality : 0.044 0.154 545 Planarity : 0.003 0.027 586 Dihedral : 4.805 18.866 463 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -1.67 (0.41), residues: 427 helix: -0.02 (0.50), residues: 114 sheet: -0.97 (0.43), residues: 159 loop : -1.93 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE L 91 TYR 0.014 0.002 TYR L 49 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 121) hydrogen bonds : angle 5.01520 ( 351) SS BOND : bond 0.00416 ( 4) SS BOND : angle 0.60198 ( 8) covalent geometry : bond 0.00431 ( 3467) covalent geometry : angle 0.54263 ( 4700) *********************** 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 82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.428 Fit side-chains REVERT: H 38 LYS cc_start: 0.8311 (tttt) cc_final: 0.7780 (tptp) outliers start: 21 outliers final: 15 residues processed: 76 average time/residue: 0.1404 time to fit residues: 13.5281 Evaluate side-chains 76 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 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 12 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147068 restraints weight = 4219.402| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.13 r_work: 0.3385 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3471 Z= 0.173 Angle : 0.544 5.467 4708 Z= 0.280 Chirality : 0.044 0.171 545 Planarity : 0.003 0.027 586 Dihedral : 4.818 18.859 463 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -1.65 (0.41), residues: 427 helix: 0.12 (0.50), residues: 113 sheet: -1.05 (0.42), residues: 159 loop : -1.90 (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 0.013 0.002 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 121) hydrogen bonds : angle 5.03452 ( 351) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.71911 ( 8) covalent geometry : bond 0.00422 ( 3467) covalent geometry : angle 0.54342 ( 4700) *********************** 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 84 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.367 Fit side-chains REVERT: H 38 LYS cc_start: 0.8300 (tttt) cc_final: 0.7848 (tptp) outliers start: 20 outliers final: 17 residues processed: 77 average time/residue: 0.1397 time to fit residues: 13.5802 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.174582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147493 restraints weight = 4195.852| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.11 r_work: 0.3394 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3471 Z= 0.153 Angle : 0.521 5.393 4708 Z= 0.269 Chirality : 0.044 0.176 545 Planarity : 0.003 0.028 586 Dihedral : 4.735 19.042 463 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.92 % Allowed : 21.24 % Favored : 73.83 % 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: -1.60 (0.41), residues: 427 helix: 0.24 (0.50), residues: 113 sheet: -1.03 (0.43), residues: 159 loop : -1.92 (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 0.013 0.001 TYR L 49 ARG 0.001 0.000 ARG C 213 Details of bonding type rmsd hydrogen bonds : bond 0.02747 ( 121) hydrogen bonds : angle 4.96649 ( 351) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.67352 ( 8) covalent geometry : bond 0.00377 ( 3467) covalent geometry : angle 0.52028 ( 4700) *********************** 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 82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.413 Fit side-chains REVERT: H 38 LYS cc_start: 0.8261 (tttt) cc_final: 0.7822 (tptp) REVERT: H 87 LYS cc_start: 0.7172 (mtmt) cc_final: 0.6371 (mmmt) REVERT: L 78 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5765 (tt) REVERT: C 222 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7756 (tt0) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.1414 time to fit residues: 13.5871 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 L residue 78 LEU Chi-restraints excluded: chain C residue 58 THR 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 6 optimal weight: 0.0870 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.178366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151699 restraints weight = 4125.302| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.09 r_work: 0.3449 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3471 Z= 0.096 Angle : 0.468 5.416 4708 Z= 0.243 Chirality : 0.043 0.170 545 Planarity : 0.003 0.028 586 Dihedral : 4.418 18.877 463 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.15 % Allowed : 22.02 % Favored : 73.83 % 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: -1.24 (0.41), residues: 427 helix: 0.72 (0.52), residues: 110 sheet: -0.87 (0.43), residues: 155 loop : -1.75 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 PHE 0.010 0.001 PHE L 46 TYR 0.014 0.001 TYR L 49 ARG 0.001 0.000 ARG C 213 Details of bonding type rmsd hydrogen bonds : bond 0.02357 ( 121) hydrogen bonds : angle 4.72048 ( 351) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.48697 ( 8) covalent geometry : bond 0.00237 ( 3467) covalent geometry : angle 0.46762 ( 4700) *********************** 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 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.397 Fit side-chains REVERT: H 38 LYS cc_start: 0.8243 (tttt) cc_final: 0.7786 (tptp) REVERT: H 87 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6374 (mmmt) REVERT: C 268 ASN cc_start: 0.8163 (m-40) cc_final: 0.7794 (t0) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.1434 time to fit residues: 13.3716 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 L residue 47 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 214 ILE 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 28 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.175706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148582 restraints weight = 4040.888| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.12 r_work: 0.3383 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3471 Z= 0.145 Angle : 0.516 5.369 4708 Z= 0.264 Chirality : 0.043 0.178 545 Planarity : 0.003 0.029 586 Dihedral : 4.546 18.605 463 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.15 % Allowed : 20.73 % Favored : 75.13 % 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: -1.26 (0.42), residues: 427 helix: 0.65 (0.52), residues: 110 sheet: -0.87 (0.43), residues: 156 loop : -1.74 (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 0.016 0.001 TYR L 49 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 121) hydrogen bonds : angle 4.89704 ( 351) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.56249 ( 8) covalent geometry : bond 0.00359 ( 3467) covalent geometry : angle 0.51621 ( 4700) *********************** 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 79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.406 Fit side-chains REVERT: H 38 LYS cc_start: 0.8240 (tttt) cc_final: 0.7763 (tptp) REVERT: H 87 LYS cc_start: 0.7110 (mtmt) cc_final: 0.6326 (mmmt) REVERT: L 78 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5769 (tt) REVERT: C 268 ASN cc_start: 0.8176 (m-40) cc_final: 0.7797 (t0) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.1440 time to fit residues: 13.3946 Evaluate side-chains 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 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 113 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 10 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.173942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146439 restraints weight = 4160.698| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.15 r_work: 0.3521 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3471 Z= 0.135 Angle : 0.513 5.370 4708 Z= 0.264 Chirality : 0.043 0.197 545 Planarity : 0.003 0.029 586 Dihedral : 4.574 19.509 463 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.15 % Allowed : 20.98 % 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: -1.23 (0.42), residues: 427 helix: 0.67 (0.52), residues: 110 sheet: -0.88 (0.44), residues: 156 loop : -1.69 (0.48), 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 0.016 0.001 TYR L 49 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.02599 ( 121) hydrogen bonds : angle 4.95952 ( 351) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.57861 ( 8) covalent geometry : bond 0.00334 ( 3467) covalent geometry : angle 0.51332 ( 4700) ********************** 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 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.366 Fit side-chains REVERT: H 38 LYS cc_start: 0.8222 (tttt) cc_final: 0.7803 (tptp) REVERT: H 87 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6410 (mmmt) REVERT: L 78 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5822 (tt) REVERT: C 268 ASN cc_start: 0.8178 (m-40) cc_final: 0.7822 (t0) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.1299 time to fit residues: 12.6543 Evaluate side-chains 81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149571 restraints weight = 4168.797| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.06 r_work: 0.3401 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3471 Z= 0.136 Angle : 0.528 5.337 4708 Z= 0.276 Chirality : 0.043 0.194 545 Planarity : 0.003 0.030 586 Dihedral : 4.533 18.815 463 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.89 % Allowed : 21.24 % 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: -1.23 (0.42), residues: 427 helix: 0.67 (0.52), residues: 110 sheet: -0.86 (0.44), residues: 156 loop : -1.70 (0.48), residues: 161 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 0.011 0.001 PHE L 91 TYR 0.015 0.001 TYR L 49 ARG 0.001 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 121) hydrogen bonds : angle 4.92186 ( 351) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.57425 ( 8) covalent geometry : bond 0.00332 ( 3467) covalent geometry : angle 0.52763 ( 4700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.29 seconds wall clock time: 39 minutes 41.66 seconds (2381.66 seconds total)