Starting phenix.real_space_refine on Tue Feb 11 02:06:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmh_45748/02_2025/9cmh_45748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmh_45748/02_2025/9cmh_45748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cmh_45748/02_2025/9cmh_45748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmh_45748/02_2025/9cmh_45748.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmh_45748/02_2025/9cmh_45748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmh_45748/02_2025/9cmh_45748.cif" } resolution = 4.0 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= 0.010 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 2270 2.51 5 N 582 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3553 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2229 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 7, 'TRANS': 278} Time building chain proxies: 2.90, per 1000 atoms: 0.82 Number of scatterers: 3553 At special positions: 0 Unit cell: (65.994, 51.76, 148.81, 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 683 8.00 N 582 7.00 C 2270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " 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: 0.82 Conformation dependent library (CDL) restraints added in 457.0 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 31.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 27 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.928A pdb=" N ALA A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 77 through 104 removed outlier: 3.593A pdb=" N CYS A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 184 Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.624A pdb=" N ILE B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.788A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61 removed outlier: 6.313A pdb=" N VAL B 57 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA B 134 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 59 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 61 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 138 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 195 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 83 removed outlier: 4.571A pdb=" N GLY B 153 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 155 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 139 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 135 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 161 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR B 133 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 163 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 131 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 165 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 129 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 127 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 138 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.575A pdb=" N LEU B 240 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE B 263 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 254 removed outlier: 3.788A pdb=" N LEU B 291 " --> pdb=" O GLN B 249 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 468 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: 0.93 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1133 1.34 - 1.46: 688 1.46 - 1.58: 1771 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3619 Sorted by residual: bond pdb=" CB VAL A 90 " pdb=" CG1 VAL A 90 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU A 130 " pdb=" CD2 LEU A 130 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 bond pdb=" CB GLN A 156 " pdb=" CG GLN A 156 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA MET A 22 " pdb=" CB MET A 22 " ideal model delta sigma weight residual 1.528 1.548 -0.019 1.56e-02 4.11e+03 1.55e+00 bond pdb=" CB MET A 62 " pdb=" CG MET A 62 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 3614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 4856 2.89 - 5.78: 53 5.78 - 8.68: 8 8.68 - 11.57: 5 11.57 - 14.46: 1 Bond angle restraints: 4923 Sorted by residual: angle pdb=" CB MET A 22 " pdb=" CG MET A 22 " pdb=" SD MET A 22 " ideal model delta sigma weight residual 112.70 127.16 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CA MET A 22 " pdb=" CB MET A 22 " pdb=" CG MET A 22 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 angle pdb=" N MET A 22 " pdb=" CA MET A 22 " pdb=" CB MET A 22 " ideal model delta sigma weight residual 110.12 115.80 -5.68 1.47e+00 4.63e-01 1.50e+01 angle pdb=" CB MET A 62 " pdb=" CG MET A 62 " pdb=" SD MET A 62 " ideal model delta sigma weight residual 112.70 123.91 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLN A 156 " pdb=" CB GLN A 156 " pdb=" CG GLN A 156 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 ... (remaining 4918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 1827 14.05 - 28.10: 203 28.10 - 42.15: 70 42.15 - 56.20: 13 56.20 - 70.25: 15 Dihedral angle restraints: 2128 sinusoidal: 793 harmonic: 1335 Sorted by residual: dihedral pdb=" CA MET A 131 " pdb=" C MET A 131 " pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO A 28 " pdb=" C PRO A 28 " pdb=" N MET A 29 " pdb=" CA MET A 29 " ideal model delta harmonic sigma weight residual 180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA MET A 62 " pdb=" C MET A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 358 0.034 - 0.067: 145 0.067 - 0.100: 46 0.100 - 0.134: 22 0.134 - 0.167: 8 Chirality restraints: 579 Sorted by residual: chirality pdb=" CA MET A 22 " pdb=" N MET A 22 " pdb=" C MET A 22 " pdb=" CB MET A 22 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CB VAL A 132 " pdb=" CA VAL A 132 " pdb=" CG1 VAL A 132 " pdb=" CG2 VAL A 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 576 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 75 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN A 75 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 75 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 76 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 81 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL B 81 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 81 " 0.012 2.00e-02 2.50e+03 pdb=" N SER B 82 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 224 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR B 224 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 224 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 224 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 224 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 224 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 224 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 224 " 0.000 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 71 2.65 - 3.22: 3684 3.22 - 3.78: 6189 3.78 - 4.34: 8430 4.34 - 4.90: 12976 Nonbonded interactions: 31350 Sorted by model distance: nonbonded pdb=" OG SER B 60 " pdb=" OH TYR B 129 " model vdw 2.092 3.040 nonbonded pdb=" O TYR B 232 " pdb=" OH TYR B 306 " model vdw 2.106 3.040 nonbonded pdb=" NE2 GLN B 140 " pdb=" OD1 ASP B 152 " model vdw 2.162 3.120 nonbonded pdb=" O ASP B 39 " pdb=" OH TYR B 264 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 135 " pdb=" O THR B 159 " model vdw 2.166 3.040 ... (remaining 31345 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3619 Z= 0.250 Angle : 0.873 14.461 4923 Z= 0.477 Chirality : 0.046 0.167 579 Planarity : 0.004 0.029 618 Dihedral : 14.789 70.254 1275 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.77 % Allowed : 24.81 % Favored : 74.42 % 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: -1.26 (0.39), residues: 462 helix: 1.65 (0.44), residues: 138 sheet: -2.12 (0.44), residues: 116 loop : -1.76 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.002 0.001 HIS B 241 PHE 0.014 0.002 PHE B 268 TYR 0.025 0.002 TYR B 224 ARG 0.003 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8544 (mm) cc_final: 0.8105 (pp) REVERT: A 48 GLU cc_start: 0.6256 (tt0) cc_final: 0.5640 (tt0) REVERT: A 144 ILE cc_start: 0.6878 (mm) cc_final: 0.6590 (tt) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.2119 time to fit residues: 12.4081 Evaluate side-chains 43 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 247 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.0060 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.091055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.079568 restraints weight = 22224.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.081243 restraints weight = 13667.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.082394 restraints weight = 9757.720| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3619 Z= 0.181 Angle : 0.614 8.442 4923 Z= 0.321 Chirality : 0.043 0.134 579 Planarity : 0.004 0.051 618 Dihedral : 5.513 52.979 500 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.79 % Allowed : 20.46 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.40), residues: 462 helix: 2.06 (0.45), residues: 138 sheet: -2.05 (0.47), residues: 113 loop : -1.84 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.002 0.001 HIS A 141 PHE 0.012 0.001 PHE B 268 TYR 0.011 0.002 TYR B 130 ARG 0.003 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.6786 (tt0) cc_final: 0.6582 (tt0) REVERT: A 118 MET cc_start: 0.4382 (ptt) cc_final: 0.3867 (ptt) REVERT: B 157 LYS cc_start: 0.8064 (tttt) cc_final: 0.7750 (ptmt) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.1869 time to fit residues: 11.0385 Evaluate side-chains 40 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.0010 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.087548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.076214 restraints weight = 22660.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.077885 restraints weight = 13935.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.078997 restraints weight = 9885.122| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3619 Z= 0.241 Angle : 0.649 8.634 4923 Z= 0.337 Chirality : 0.045 0.266 579 Planarity : 0.004 0.041 618 Dihedral : 4.721 17.114 496 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.84 % Allowed : 21.48 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.39), residues: 462 helix: 2.11 (0.44), residues: 133 sheet: -2.02 (0.48), residues: 108 loop : -1.85 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.003 0.001 HIS B 285 PHE 0.010 0.001 PHE B 104 TYR 0.008 0.002 TYR B 136 ARG 0.004 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9455 (tp) cc_final: 0.9215 (tp) REVERT: A 18 TRP cc_start: 0.6258 (t60) cc_final: 0.5873 (t60) REVERT: A 19 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8266 (pp) REVERT: A 31 ARG cc_start: 0.6203 (ttm170) cc_final: 0.5382 (ttm170) REVERT: A 48 GLU cc_start: 0.6715 (tt0) cc_final: 0.6472 (tt0) REVERT: A 118 MET cc_start: 0.4071 (ptt) cc_final: 0.3499 (ptt) REVERT: B 157 LYS cc_start: 0.8071 (tttt) cc_final: 0.7863 (ptmt) REVERT: B 315 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6767 (pp) outliers start: 15 outliers final: 7 residues processed: 48 average time/residue: 0.1912 time to fit residues: 11.3759 Evaluate side-chains 45 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 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 = 0.4171 r_free = 0.4171 target = 0.088975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.077563 restraints weight = 22484.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.079276 restraints weight = 13836.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.080392 restraints weight = 9769.684| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3619 Z= 0.164 Angle : 0.630 10.653 4923 Z= 0.321 Chirality : 0.044 0.257 579 Planarity : 0.003 0.030 618 Dihedral : 4.525 16.097 496 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.07 % Allowed : 21.74 % Favored : 75.19 % 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: -0.93 (0.40), residues: 462 helix: 2.32 (0.45), residues: 133 sheet: -2.01 (0.48), residues: 113 loop : -1.75 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.001 0.000 HIS B 241 PHE 0.014 0.001 PHE B 316 TYR 0.008 0.001 TYR B 133 ARG 0.003 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9435 (tp) cc_final: 0.9208 (tp) REVERT: A 18 TRP cc_start: 0.6193 (t60) cc_final: 0.5815 (t60) REVERT: A 19 LEU cc_start: 0.8816 (mm) cc_final: 0.8385 (pp) REVERT: A 31 ARG cc_start: 0.6200 (ttm170) cc_final: 0.4741 (ttm170) REVERT: A 48 GLU cc_start: 0.6703 (tt0) cc_final: 0.6490 (tt0) REVERT: A 52 MET cc_start: 0.8901 (ppp) cc_final: 0.8490 (ppp) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 0.1606 time to fit residues: 9.7256 Evaluate side-chains 42 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 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 = 0.4129 r_free = 0.4129 target = 0.086725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.075422 restraints weight = 22748.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.076985 restraints weight = 14207.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.078102 restraints weight = 10160.834| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3619 Z= 0.218 Angle : 0.642 10.020 4923 Z= 0.327 Chirality : 0.043 0.205 579 Planarity : 0.003 0.029 618 Dihedral : 4.562 16.836 496 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.12 % Allowed : 20.72 % Favored : 74.17 % 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: -0.91 (0.40), residues: 462 helix: 2.28 (0.45), residues: 133 sheet: -1.63 (0.52), residues: 96 loop : -1.95 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.003 0.001 HIS B 285 PHE 0.030 0.002 PHE B 316 TYR 0.021 0.002 TYR B 224 ARG 0.003 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.6037 (t60) cc_final: 0.5813 (t60) REVERT: A 19 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 52 MET cc_start: 0.8939 (ppp) cc_final: 0.8375 (ppp) REVERT: B 244 ILE cc_start: 0.1413 (OUTLIER) cc_final: 0.1039 (mp) outliers start: 20 outliers final: 11 residues processed: 54 average time/residue: 0.1574 time to fit residues: 10.7012 Evaluate side-chains 48 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 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 = 0.4118 r_free = 0.4118 target = 0.086389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.074956 restraints weight = 23024.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.076601 restraints weight = 13956.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.077707 restraints weight = 9847.743| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3619 Z= 0.197 Angle : 0.628 9.638 4923 Z= 0.321 Chirality : 0.043 0.193 579 Planarity : 0.003 0.028 618 Dihedral : 4.547 16.550 496 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.37 % Allowed : 22.25 % Favored : 72.38 % 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: -0.87 (0.39), residues: 462 helix: 2.27 (0.45), residues: 133 sheet: -1.47 (0.53), residues: 96 loop : -1.97 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.002 0.001 HIS B 285 PHE 0.015 0.001 PHE B 316 TYR 0.022 0.002 TYR B 224 ARG 0.005 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.6000 (t60) cc_final: 0.5789 (t60) REVERT: A 19 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 52 MET cc_start: 0.8915 (ppp) cc_final: 0.8646 (ppp) REVERT: B 252 ARG cc_start: 0.4641 (OUTLIER) cc_final: 0.2946 (ptm160) REVERT: B 300 MET cc_start: 0.7813 (pmm) cc_final: 0.7478 (pmm) outliers start: 21 outliers final: 11 residues processed: 56 average time/residue: 0.1696 time to fit residues: 11.7696 Evaluate side-chains 50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.085262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.074063 restraints weight = 22614.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.075601 restraints weight = 13973.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.076619 restraints weight = 9990.903| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3619 Z= 0.215 Angle : 0.669 11.178 4923 Z= 0.334 Chirality : 0.043 0.180 579 Planarity : 0.003 0.025 618 Dihedral : 4.617 16.912 496 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.60 % Allowed : 23.27 % Favored : 72.12 % 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: -0.88 (0.40), residues: 462 helix: 2.25 (0.46), residues: 133 sheet: -1.70 (0.48), residues: 111 loop : -1.82 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.003 0.001 HIS B 285 PHE 0.010 0.001 PHE B 316 TYR 0.028 0.002 TYR B 224 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8343 (tp) REVERT: B 252 ARG cc_start: 0.5020 (OUTLIER) cc_final: 0.3290 (ptm160) REVERT: B 300 MET cc_start: 0.7958 (pmm) cc_final: 0.7676 (pmm) outliers start: 18 outliers final: 10 residues processed: 53 average time/residue: 0.1521 time to fit residues: 10.2356 Evaluate side-chains 46 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 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 = 0.4094 r_free = 0.4094 target = 0.084736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.073552 restraints weight = 23167.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.075093 restraints weight = 14492.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.076107 restraints weight = 10354.217| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3619 Z= 0.228 Angle : 0.670 10.456 4923 Z= 0.346 Chirality : 0.044 0.240 579 Planarity : 0.004 0.025 618 Dihedral : 4.606 16.978 496 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.60 % Allowed : 23.79 % Favored : 71.61 % 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: -0.89 (0.39), residues: 462 helix: 2.28 (0.45), residues: 133 sheet: -1.70 (0.47), residues: 110 loop : -1.86 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 18 HIS 0.003 0.001 HIS B 285 PHE 0.006 0.001 PHE B 104 TYR 0.034 0.002 TYR B 296 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8448 (tp) REVERT: B 252 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.3399 (ptm160) REVERT: B 300 MET cc_start: 0.7946 (pmm) cc_final: 0.7643 (pmm) outliers start: 18 outliers final: 11 residues processed: 51 average time/residue: 0.1541 time to fit residues: 10.0055 Evaluate side-chains 49 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** 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 = 0.4097 r_free = 0.4097 target = 0.084227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.073340 restraints weight = 22482.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.074805 restraints weight = 14110.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.075833 restraints weight = 10173.888| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3619 Z= 0.214 Angle : 0.700 12.693 4923 Z= 0.350 Chirality : 0.044 0.170 579 Planarity : 0.003 0.025 618 Dihedral : 4.676 17.178 496 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.84 % Allowed : 23.79 % Favored : 72.38 % 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: -0.95 (0.39), residues: 462 helix: 2.13 (0.46), residues: 133 sheet: -1.72 (0.47), residues: 110 loop : -1.82 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 18 HIS 0.002 0.001 HIS B 285 PHE 0.005 0.001 PHE B 104 TYR 0.032 0.002 TYR B 296 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8221 (tp) REVERT: B 252 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.3399 (ptm160) REVERT: B 300 MET cc_start: 0.7876 (pmm) cc_final: 0.7622 (pmm) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 0.1645 time to fit residues: 10.2637 Evaluate side-chains 49 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.082832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.071975 restraints weight = 22768.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.073401 restraints weight = 14270.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.074400 restraints weight = 10282.846| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3619 Z= 0.269 Angle : 0.750 12.313 4923 Z= 0.375 Chirality : 0.044 0.151 579 Planarity : 0.004 0.026 618 Dihedral : 4.857 18.413 496 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.84 % Allowed : 23.53 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.39), residues: 462 helix: 1.99 (0.45), residues: 133 sheet: -1.82 (0.46), residues: 110 loop : -1.86 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 18 HIS 0.003 0.001 HIS B 285 PHE 0.008 0.001 PHE A 35 TYR 0.034 0.003 TYR B 296 ARG 0.005 0.001 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8301 (tp) REVERT: B 252 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.3491 (ptm160) REVERT: B 300 MET cc_start: 0.7876 (pmm) cc_final: 0.7629 (pmm) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.1657 time to fit residues: 10.7374 Evaluate side-chains 51 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** 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 = 0.4112 r_free = 0.4112 target = 0.085003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.074029 restraints weight = 22723.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.075593 restraints weight = 13928.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.076617 restraints weight = 9906.329| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3619 Z= 0.198 Angle : 0.793 15.919 4923 Z= 0.375 Chirality : 0.044 0.145 579 Planarity : 0.003 0.027 618 Dihedral : 4.726 17.551 496 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.84 % Allowed : 23.79 % Favored : 72.38 % 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: -0.98 (0.39), residues: 462 helix: 1.97 (0.45), residues: 133 sheet: -1.69 (0.47), residues: 110 loop : -1.77 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 18 HIS 0.002 0.001 HIS B 285 PHE 0.007 0.001 PHE A 35 TYR 0.025 0.002 TYR B 224 ARG 0.004 0.001 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.14 seconds wall clock time: 27 minutes 58.73 seconds (1678.73 seconds total)