Starting phenix.real_space_refine on Fri May 9 13:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vja_43278/05_2025/8vja_43278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vja_43278/05_2025/8vja_43278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vja_43278/05_2025/8vja_43278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vja_43278/05_2025/8vja_43278.map" model { file = "/net/cci-nas-00/data/ceres_data/8vja_43278/05_2025/8vja_43278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vja_43278/05_2025/8vja_43278.cif" } resolution = 2.7 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1322 2.51 5 N 357 2.21 5 O 424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2113 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2113 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 266} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 6.50, per 1000 atoms: 3.08 Number of scatterers: 2113 At special positions: 0 Unit cell: (77.9, 104.14, 62.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 424 8.00 N 357 7.00 C 1322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.47 Conformation dependent library (CDL) restraints added in 272.7 milliseconds 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 502 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 5 sheets defined 5.1% alpha, 48.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.977A pdb=" N VAL A 213 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER A 237 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 215 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A 235 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 221 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS A 229 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 235 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLN A 71 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER A 64 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS A 51 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU A 66 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU A 49 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 68 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 45 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.977A pdb=" N VAL A 213 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER A 237 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 215 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A 235 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 221 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS A 229 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 97 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 108 removed outlier: 5.604A pdb=" N TYR A 196 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 105 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 194 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A 107 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 192 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 134 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.575A pdb=" N ARG A 115 " --> pdb=" O ILE A 179 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 204 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: 0.58 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 373 1.30 - 1.43: 577 1.43 - 1.56: 1183 1.56 - 1.69: 0 1.69 - 1.82: 19 Bond restraints: 2152 Sorted by residual: bond pdb=" C ASN A 230 " pdb=" O ASN A 230 " ideal model delta sigma weight residual 1.234 1.167 0.068 1.22e-02 6.72e+03 3.07e+01 bond pdb=" C LYS A 229 " pdb=" O LYS A 229 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.22e-02 6.72e+03 1.21e+01 bond pdb=" CA TYR A 5 " pdb=" C TYR A 5 " ideal model delta sigma weight residual 1.521 1.481 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" C ASP A 19 " pdb=" O ASP A 19 " ideal model delta sigma weight residual 1.235 1.202 0.034 1.14e-02 7.69e+03 8.67e+00 bond pdb=" CZ ARG A 269 " pdb=" NH2 ARG A 269 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 7.98e+00 ... (remaining 2147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 1963 1.57 - 3.14: 757 3.14 - 4.71: 166 4.71 - 6.28: 35 6.28 - 7.86: 6 Bond angle restraints: 2927 Sorted by residual: angle pdb=" N ARG A 176 " pdb=" CA ARG A 176 " pdb=" C ARG A 176 " ideal model delta sigma weight residual 108.90 116.76 -7.86 1.63e+00 3.76e-01 2.32e+01 angle pdb=" N HIS A 56 " pdb=" CA HIS A 56 " pdb=" C HIS A 56 " ideal model delta sigma weight residual 108.99 116.43 -7.44 1.57e+00 4.06e-01 2.25e+01 angle pdb=" C ASP A 222 " pdb=" N ASN A 223 " pdb=" CA ASN A 223 " ideal model delta sigma weight residual 120.65 126.89 -6.24 1.36e+00 5.41e-01 2.10e+01 angle pdb=" N ARG A 218 " pdb=" CA ARG A 218 " pdb=" C ARG A 218 " ideal model delta sigma weight residual 108.48 115.80 -7.32 1.80e+00 3.09e-01 1.65e+01 angle pdb=" N TYR A 5 " pdb=" CA TYR A 5 " pdb=" C TYR A 5 " ideal model delta sigma weight residual 109.24 102.47 6.77 1.67e+00 3.59e-01 1.64e+01 ... (remaining 2922 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.25: 1134 16.25 - 32.50: 101 32.50 - 48.74: 26 48.74 - 64.99: 6 64.99 - 81.23: 1 Dihedral angle restraints: 1268 sinusoidal: 477 harmonic: 791 Sorted by residual: dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N ALA A 69 " pdb=" CA ALA A 69 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA LEU A 67 " pdb=" C LEU A 67 " pdb=" N GLU A 68 " pdb=" CA GLU A 68 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA THR A 96 " pdb=" C THR A 96 " pdb=" N THR A 97 " pdb=" CA THR A 97 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 1265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 170 0.065 - 0.130: 111 0.130 - 0.195: 37 0.195 - 0.259: 9 0.259 - 0.324: 2 Chirality restraints: 329 Sorted by residual: chirality pdb=" CA CYS A 77 " pdb=" N CYS A 77 " pdb=" C CYS A 77 " pdb=" CB CYS A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB THR A 41 " pdb=" CA THR A 41 " pdb=" OG1 THR A 41 " pdb=" CG2 THR A 41 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" C PRO A 164 " pdb=" CB PRO A 164 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 326 not shown) Planarity restraints: 388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 117 " -0.087 2.00e-02 2.50e+03 4.71e-02 4.44e+01 pdb=" CG TYR A 117 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 117 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR A 117 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 117 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 117 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 117 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 117 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 196 " 0.079 2.00e-02 2.50e+03 4.54e-02 4.12e+01 pdb=" CG TYR A 196 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 196 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 196 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 196 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 196 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 196 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 196 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 9 " -0.074 2.00e-02 2.50e+03 4.15e-02 3.45e+01 pdb=" CG TYR A 9 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 9 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 9 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 9 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 9 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 9 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 9 " -0.067 2.00e-02 2.50e+03 ... (remaining 385 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1049 3.01 - 3.48: 1906 3.48 - 3.95: 3287 3.95 - 4.43: 3462 4.43 - 4.90: 6216 Nonbonded interactions: 15920 Sorted by model distance: nonbonded pdb=" OD1 ASP A 103 " pdb=" NE2 GLN A 195 " model vdw 2.535 3.120 nonbonded pdb=" OD1 ASP A 19 " pdb=" O ALA A 216 " model vdw 2.559 3.040 nonbonded pdb=" OE1 GLU A 106 " pdb=" OH TYR A 196 " model vdw 2.581 3.040 nonbonded pdb=" OE2 GLU A 31 " pdb=" NH1 ARG A 218 " model vdw 2.583 3.120 nonbonded pdb=" OG1 THR A 133 " pdb=" OD1 ASP A 199 " model vdw 2.587 3.040 ... (remaining 15915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 10.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 15.480 Find NCS groups from input model: 0.020 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.012 0.068 2152 Z= 0.695 Angle : 1.734 7.856 2927 Z= 1.137 Chirality : 0.091 0.324 329 Planarity : 0.010 0.047 388 Dihedral : 14.095 81.235 766 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 4.87 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.42), residues: 273 helix: -0.74 (1.53), residues: 10 sheet: 0.57 (0.46), residues: 95 loop : -1.15 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.018 TRP A 88 HIS 0.007 0.004 HIS A 51 PHE 0.034 0.011 PHE A 18 TYR 0.087 0.018 TYR A 117 ARG 0.005 0.001 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.16178 ( 66) hydrogen bonds : angle 8.39536 ( 204) covalent geometry : bond 0.01158 ( 2152) covalent geometry : angle 1.73375 ( 2927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.8290 (m) cc_final: 0.7815 (p) REVERT: A 59 ARG cc_start: 0.8054 (mmt90) cc_final: 0.5465 (mtt180) REVERT: A 259 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7924 (tppt) outliers start: 9 outliers final: 2 residues processed: 59 average time/residue: 1.2939 time to fit residues: 77.7231 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 195 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113556 restraints weight = 2939.344| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.70 r_work: 0.3396 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2152 Z= 0.142 Angle : 0.576 5.136 2927 Z= 0.331 Chirality : 0.045 0.141 329 Planarity : 0.004 0.032 388 Dihedral : 6.726 43.770 307 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.19 % Allowed : 12.39 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.44), residues: 273 helix: 0.53 (1.80), residues: 10 sheet: 0.35 (0.42), residues: 106 loop : -0.93 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.002 0.001 HIS A 56 PHE 0.010 0.002 PHE A 75 TYR 0.009 0.001 TYR A 33 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 66) hydrogen bonds : angle 6.00707 ( 204) covalent geometry : bond 0.00297 ( 2152) covalent geometry : angle 0.57591 ( 2927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.201 Fit side-chains REVERT: A 100 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6690 (tp40) outliers start: 14 outliers final: 4 residues processed: 43 average time/residue: 1.0019 time to fit residues: 44.1974 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 222 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.137071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108012 restraints weight = 2948.487| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.84 r_work: 0.3344 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 2152 Z= 0.202 Angle : 0.591 4.589 2927 Z= 0.333 Chirality : 0.047 0.149 329 Planarity : 0.004 0.043 388 Dihedral : 5.503 15.226 300 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.08 % Allowed : 12.83 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.44), residues: 273 helix: 0.51 (1.81), residues: 10 sheet: 0.14 (0.43), residues: 106 loop : -1.02 (0.42), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 251 HIS 0.003 0.001 HIS A 56 PHE 0.009 0.002 PHE A 258 TYR 0.011 0.002 TYR A 5 ARG 0.003 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 66) hydrogen bonds : angle 5.82367 ( 204) covalent geometry : bond 0.00458 ( 2152) covalent geometry : angle 0.59088 ( 2927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.248 Fit side-chains REVERT: A 68 GLU cc_start: 0.8615 (pt0) cc_final: 0.8353 (pt0) REVERT: A 71 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: A 92 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: A 100 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6798 (tp40) REVERT: A 130 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.5682 (mpp-170) outliers start: 16 outliers final: 6 residues processed: 41 average time/residue: 1.2832 time to fit residues: 53.7331 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110068 restraints weight = 2913.729| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.79 r_work: 0.3380 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2152 Z= 0.132 Angle : 0.527 5.686 2927 Z= 0.297 Chirality : 0.045 0.134 329 Planarity : 0.004 0.062 388 Dihedral : 5.085 16.003 300 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.19 % Allowed : 14.16 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.45), residues: 273 helix: 0.67 (1.82), residues: 10 sheet: 0.28 (0.46), residues: 100 loop : -0.85 (0.42), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 251 HIS 0.002 0.001 HIS A 56 PHE 0.007 0.001 PHE A 258 TYR 0.006 0.001 TYR A 5 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 66) hydrogen bonds : angle 5.51745 ( 204) covalent geometry : bond 0.00285 ( 2152) covalent geometry : angle 0.52674 ( 2927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.242 Fit side-chains REVERT: A 68 GLU cc_start: 0.8512 (pt0) cc_final: 0.8253 (pt0) REVERT: A 71 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: A 100 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6731 (tp40) REVERT: A 130 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.5435 (mpp-170) outliers start: 14 outliers final: 5 residues processed: 46 average time/residue: 1.1173 time to fit residues: 52.5882 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 183 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 overall best weight: 2.3804 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.137442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109146 restraints weight = 2983.996| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.83 r_work: 0.3337 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 2152 Z= 0.229 Angle : 0.596 5.402 2927 Z= 0.331 Chirality : 0.047 0.145 329 Planarity : 0.004 0.053 388 Dihedral : 5.292 18.088 300 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.19 % Allowed : 14.16 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.45), residues: 273 helix: 0.43 (1.78), residues: 10 sheet: -0.04 (0.45), residues: 106 loop : -0.91 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 88 HIS 0.003 0.001 HIS A 56 PHE 0.009 0.002 PHE A 258 TYR 0.009 0.002 TYR A 117 ARG 0.004 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 66) hydrogen bonds : angle 5.63954 ( 204) covalent geometry : bond 0.00527 ( 2152) covalent geometry : angle 0.59591 ( 2927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.219 Fit side-chains REVERT: A 68 GLU cc_start: 0.8651 (pt0) cc_final: 0.7439 (tp30) REVERT: A 71 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: A 97 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7748 (t) REVERT: A 130 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.5808 (mpp-170) REVERT: A 227 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8726 (mp) outliers start: 14 outliers final: 6 residues processed: 44 average time/residue: 1.1052 time to fit residues: 49.7618 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.140547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113329 restraints weight = 2968.793| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.76 r_work: 0.3404 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2152 Z= 0.119 Angle : 0.510 5.133 2927 Z= 0.283 Chirality : 0.044 0.130 329 Planarity : 0.004 0.044 388 Dihedral : 4.729 16.673 300 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.87 % Allowed : 17.26 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.46), residues: 273 helix: 0.72 (1.76), residues: 10 sheet: -0.02 (0.47), residues: 100 loop : -0.86 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 HIS 0.001 0.001 HIS A 56 PHE 0.007 0.001 PHE A 258 TYR 0.008 0.001 TYR A 168 ARG 0.001 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 66) hydrogen bonds : angle 5.27813 ( 204) covalent geometry : bond 0.00268 ( 2152) covalent geometry : angle 0.51032 ( 2927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.220 Fit side-chains REVERT: A 68 GLU cc_start: 0.8520 (pt0) cc_final: 0.7458 (tp30) REVERT: A 71 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: A 100 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6703 (tp40) REVERT: A 130 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.5689 (mpp-170) outliers start: 11 outliers final: 4 residues processed: 39 average time/residue: 1.2139 time to fit residues: 48.3667 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.137761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109518 restraints weight = 3009.784| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.80 r_work: 0.3318 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2152 Z= 0.202 Angle : 0.566 5.025 2927 Z= 0.312 Chirality : 0.046 0.142 329 Planarity : 0.004 0.041 388 Dihedral : 4.999 16.486 300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.75 % Allowed : 16.37 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.46), residues: 273 helix: 0.89 (1.87), residues: 10 sheet: -0.14 (0.47), residues: 100 loop : -0.90 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 88 HIS 0.002 0.001 HIS A 56 PHE 0.009 0.002 PHE A 258 TYR 0.009 0.002 TYR A 117 ARG 0.003 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 66) hydrogen bonds : angle 5.46190 ( 204) covalent geometry : bond 0.00461 ( 2152) covalent geometry : angle 0.56579 ( 2927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.239 Fit side-chains REVERT: A 68 GLU cc_start: 0.8575 (pt0) cc_final: 0.7457 (tp30) REVERT: A 71 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: A 97 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7662 (t) REVERT: A 100 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6792 (tp40) REVERT: A 130 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.5852 (mpp-170) outliers start: 13 outliers final: 6 residues processed: 43 average time/residue: 1.1197 time to fit residues: 49.2452 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.138353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110380 restraints weight = 3050.333| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.81 r_work: 0.3339 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2152 Z= 0.152 Angle : 0.533 5.285 2927 Z= 0.295 Chirality : 0.045 0.136 329 Planarity : 0.005 0.076 388 Dihedral : 4.807 16.476 300 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.75 % Allowed : 17.70 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.47), residues: 273 helix: 0.82 (1.85), residues: 10 sheet: -0.07 (0.49), residues: 99 loop : -0.89 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 88 HIS 0.002 0.001 HIS A 56 PHE 0.008 0.001 PHE A 258 TYR 0.007 0.001 TYR A 117 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 66) hydrogen bonds : angle 5.28851 ( 204) covalent geometry : bond 0.00343 ( 2152) covalent geometry : angle 0.53296 ( 2927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.240 Fit side-chains REVERT: A 68 GLU cc_start: 0.8537 (pt0) cc_final: 0.7437 (tp30) REVERT: A 71 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: A 97 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7633 (t) REVERT: A 100 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6659 (tp40) REVERT: A 130 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.5620 (mpp-170) outliers start: 13 outliers final: 6 residues processed: 42 average time/residue: 1.1492 time to fit residues: 49.3603 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109936 restraints weight = 3002.972| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.82 r_work: 0.3355 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2152 Z= 0.160 Angle : 0.545 5.105 2927 Z= 0.300 Chirality : 0.046 0.145 329 Planarity : 0.005 0.069 388 Dihedral : 4.793 16.372 300 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.42 % Allowed : 19.47 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.48), residues: 273 helix: 0.88 (1.87), residues: 10 sheet: -0.17 (0.49), residues: 97 loop : -0.68 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 88 HIS 0.002 0.001 HIS A 56 PHE 0.008 0.001 PHE A 258 TYR 0.007 0.001 TYR A 117 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 66) hydrogen bonds : angle 5.32033 ( 204) covalent geometry : bond 0.00359 ( 2152) covalent geometry : angle 0.54473 ( 2927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.230 Fit side-chains REVERT: A 68 GLU cc_start: 0.8553 (pt0) cc_final: 0.7505 (tp30) REVERT: A 71 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: A 97 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7613 (t) REVERT: A 100 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6666 (tp40) REVERT: A 130 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.5821 (mpp-170) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 1.1764 time to fit residues: 46.9171 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111211 restraints weight = 2972.948| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.73 r_work: 0.3367 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2152 Z= 0.130 Angle : 0.536 4.820 2927 Z= 0.296 Chirality : 0.045 0.137 329 Planarity : 0.004 0.067 388 Dihedral : 4.584 18.120 300 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.87 % Allowed : 19.47 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.48), residues: 273 helix: 1.05 (1.89), residues: 10 sheet: -0.06 (0.51), residues: 97 loop : -0.60 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 HIS 0.001 0.001 HIS A 56 PHE 0.007 0.001 PHE A 258 TYR 0.008 0.001 TYR A 117 ARG 0.001 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 66) hydrogen bonds : angle 5.16231 ( 204) covalent geometry : bond 0.00291 ( 2152) covalent geometry : angle 0.53638 ( 2927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.237 Fit side-chains REVERT: A 68 GLU cc_start: 0.8526 (pt0) cc_final: 0.7475 (tp30) REVERT: A 100 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6603 (tp40) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 1.1715 time to fit residues: 47.8491 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 0.0470 chunk 18 optimal weight: 0.8980 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109018 restraints weight = 2979.261| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.86 r_work: 0.3360 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2152 Z= 0.133 Angle : 0.536 4.878 2927 Z= 0.295 Chirality : 0.045 0.145 329 Planarity : 0.004 0.065 388 Dihedral : 4.560 18.271 300 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.42 % Allowed : 19.91 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.49), residues: 273 helix: 1.11 (1.90), residues: 10 sheet: -0.03 (0.51), residues: 97 loop : -0.56 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 88 HIS 0.001 0.001 HIS A 56 PHE 0.007 0.001 PHE A 258 TYR 0.008 0.001 TYR A 117 ARG 0.001 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.02718 ( 66) hydrogen bonds : angle 5.15866 ( 204) covalent geometry : bond 0.00297 ( 2152) covalent geometry : angle 0.53584 ( 2927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2803.05 seconds wall clock time: 49 minutes 6.27 seconds (2946.27 seconds total)