Starting phenix.real_space_refine on Tue Feb 11 09:58:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6f_36003/02_2025/8j6f_36003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6f_36003/02_2025/8j6f_36003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6f_36003/02_2025/8j6f_36003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6f_36003/02_2025/8j6f_36003.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6f_36003/02_2025/8j6f_36003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6f_36003/02_2025/8j6f_36003.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1592 atoms to isotropic. 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 12 5.16 5 C 2443 2.51 5 N 657 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3870 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1590 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1615 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "I" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 571 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 3 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.03, per 1000 atoms: 1.04 Number of scatterers: 3870 At special positions: 0 Unit cell: (54.12, 64.78, 107.42, 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 12 16.00 O 758 8.00 N 657 7.00 C 2443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 Links applied NAG-ASN " NAG I 401 " - " ASN I 221 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 414.2 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 12 sheets defined 1.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.625A pdb=" N SER H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 195' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.322A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 92 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.174A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.174A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 160 removed outlier: 4.639A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.163A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.382A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 115 removed outlier: 3.732A pdb=" N CYS L 134 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 144 through 148 removed outlier: 4.265A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 220 through 223 removed outlier: 5.556A pdb=" N ASN I 221 " --> pdb=" O GLN I 239 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN I 239 " --> pdb=" O ASN I 221 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR I 237 " --> pdb=" O THR I 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 268 through 269 removed outlier: 3.623A pdb=" N GLU I 254 " --> pdb=" O ARG I 293 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 270 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: 1.09 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1065 1.33 - 1.45: 757 1.45 - 1.57: 2127 1.57 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3966 Sorted by residual: bond pdb=" C ALA H 101 " pdb=" N ARG H 102 " ideal model delta sigma weight residual 1.332 1.297 0.036 1.40e-02 5.10e+03 6.49e+00 bond pdb=" CG LEU L 94 " pdb=" CD2 LEU L 94 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.27e+00 bond pdb=" SD MET H 106 " pdb=" CE MET H 106 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.92e+00 bond pdb=" CG GLN L 90 " pdb=" CD GLN L 90 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.58e+00 bond pdb=" CA THR H 157 " pdb=" CB THR H 157 " ideal model delta sigma weight residual 1.539 1.630 -0.090 4.88e-02 4.20e+02 3.43e+00 ... (remaining 3961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 5051 1.92 - 3.83: 286 3.83 - 5.75: 42 5.75 - 7.66: 14 7.66 - 9.58: 9 Bond angle restraints: 5402 Sorted by residual: angle pdb=" C TYR L 50 " pdb=" N THR L 51 " pdb=" CA THR L 51 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CB LYS H 215 " pdb=" CG LYS H 215 " pdb=" CD LYS H 215 " ideal model delta sigma weight residual 111.30 119.08 -7.78 2.30e+00 1.89e-01 1.14e+01 angle pdb=" C TRP L 148 " pdb=" N LYS L 149 " pdb=" CA LYS L 149 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N PHE H 152 " pdb=" CA PHE H 152 " pdb=" C PHE H 152 " ideal model delta sigma weight residual 109.81 117.10 -7.29 2.21e+00 2.05e-01 1.09e+01 angle pdb=" N GLU H 154 " pdb=" CA GLU H 154 " pdb=" C GLU H 154 " ideal model delta sigma weight residual 108.97 114.84 -5.87 1.82e+00 3.02e-01 1.04e+01 ... (remaining 5397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2128 17.44 - 34.88: 203 34.88 - 52.32: 40 52.32 - 69.76: 5 69.76 - 87.19: 4 Dihedral angle restraints: 2380 sinusoidal: 935 harmonic: 1445 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 148.64 -55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA GLU I 296 " pdb=" C GLU I 296 " pdb=" N GLU I 297 " pdb=" CA GLU I 297 " ideal model delta harmonic sigma weight residual 180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PRO H 155 " pdb=" C PRO H 155 " pdb=" N VAL H 156 " pdb=" CA VAL H 156 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 373 0.045 - 0.090: 155 0.090 - 0.135: 60 0.135 - 0.180: 17 0.180 - 0.225: 6 Chirality restraints: 611 Sorted by residual: chirality pdb=" CA PHE H 152 " pdb=" N PHE H 152 " pdb=" C PHE H 152 " pdb=" CB PHE H 152 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU H 20 " pdb=" CB LEU H 20 " pdb=" CD1 LEU H 20 " pdb=" CD2 LEU H 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 608 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 61 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO H 62 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO H 62 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 62 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO L 80 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 154 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO H 155 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " -0.051 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 458 2.75 - 3.29: 3545 3.29 - 3.82: 6540 3.82 - 4.36: 7591 4.36 - 4.90: 13565 Nonbonded interactions: 31699 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 99 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR L 96 " pdb=" O PHE I 298 " model vdw 2.230 3.040 nonbonded pdb=" O ASP H 90 " pdb=" OH TYR H 94 " model vdw 2.265 3.040 nonbonded pdb=" O PRO H 173 " pdb=" OG SER L 162 " model vdw 2.273 3.040 nonbonded pdb=" O ILE L 106 " pdb=" NE2 GLN L 166 " model vdw 2.309 3.120 ... (remaining 31694 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=0.00 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: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.009 0.099 3966 Z= 0.562 Angle : 1.060 9.576 5402 Z= 0.550 Chirality : 0.060 0.225 611 Planarity : 0.011 0.125 683 Dihedral : 14.303 87.194 1434 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.18 (0.37), residues: 480 helix: -5.48 (0.27), residues: 6 sheet: -2.43 (0.34), residues: 204 loop : -1.69 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP I 238 HIS 0.010 0.002 HIS I 275 PHE 0.054 0.005 PHE I 298 TYR 0.036 0.004 TYR I 249 ARG 0.011 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.449 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1845 time to fit residues: 13.1976 Evaluate side-chains 46 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.189914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.156096 restraints weight = 3995.449| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.27 r_work: 0.3739 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3966 Z= 0.255 Angle : 0.696 12.283 5402 Z= 0.353 Chirality : 0.045 0.155 611 Planarity : 0.008 0.076 683 Dihedral : 6.125 24.567 552 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.68 % Allowed : 9.34 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.38), residues: 480 helix: -5.47 (0.28), residues: 6 sheet: -2.25 (0.33), residues: 224 loop : -1.40 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 306 HIS 0.003 0.001 HIS I 275 PHE 0.011 0.002 PHE I 298 TYR 0.015 0.002 TYR I 249 ARG 0.002 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.384 Fit side-chains REVERT: L 24 ARG cc_start: 0.6439 (mtp180) cc_final: 0.6160 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.1611 time to fit residues: 11.2290 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151047 restraints weight = 4007.982| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.26 r_work: 0.3677 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 3966 Z= 0.352 Angle : 0.717 7.008 5402 Z= 0.363 Chirality : 0.046 0.151 611 Planarity : 0.007 0.066 683 Dihedral : 6.016 25.461 552 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.14 % Allowed : 13.44 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.38), residues: 480 helix: -5.43 (0.29), residues: 6 sheet: -2.11 (0.35), residues: 209 loop : -1.44 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 306 HIS 0.005 0.001 HIS L 55 PHE 0.019 0.002 PHE L 139 TYR 0.018 0.002 TYR I 249 ARG 0.010 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.459 Fit side-chains REVERT: L 24 ARG cc_start: 0.6602 (mtp180) cc_final: 0.6307 (mtp-110) REVERT: I 295 GLN cc_start: 0.7303 (pt0) cc_final: 0.7103 (pt0) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1894 time to fit residues: 12.7599 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148274 restraints weight = 4035.385| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.26 r_work: 0.3650 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 3966 Z= 0.407 Angle : 0.725 7.288 5402 Z= 0.368 Chirality : 0.047 0.149 611 Planarity : 0.007 0.063 683 Dihedral : 6.080 26.967 552 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.82 % Allowed : 17.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.38), residues: 480 helix: -5.42 (0.29), residues: 6 sheet: -2.21 (0.35), residues: 211 loop : -1.41 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 35 HIS 0.004 0.001 HIS L 55 PHE 0.026 0.003 PHE I 298 TYR 0.020 0.002 TYR H 51 ARG 0.007 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.457 Fit side-chains REVERT: L 24 ARG cc_start: 0.6581 (mtp180) cc_final: 0.6270 (mtp-110) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1655 time to fit residues: 10.4187 Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** 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 = 0.4206 r_free = 0.4206 target = 0.185202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151176 restraints weight = 4085.885| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.29 r_work: 0.3695 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3966 Z= 0.286 Angle : 0.666 7.135 5402 Z= 0.336 Chirality : 0.045 0.183 611 Planarity : 0.007 0.060 683 Dihedral : 5.781 26.091 552 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.05 % Allowed : 18.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.39), residues: 480 helix: -5.40 (0.29), residues: 6 sheet: -2.08 (0.35), residues: 212 loop : -1.23 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 35 HIS 0.003 0.001 HIS L 55 PHE 0.031 0.002 PHE I 298 TYR 0.017 0.002 TYR H 51 ARG 0.006 0.001 ARG I 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.470 Fit side-chains REVERT: L 24 ARG cc_start: 0.6571 (mtp180) cc_final: 0.6264 (mtp-110) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1649 time to fit residues: 10.5574 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** 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 = 0.4209 r_free = 0.4209 target = 0.185650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151895 restraints weight = 4019.969| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.26 r_work: 0.3690 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3966 Z= 0.294 Angle : 0.667 8.749 5402 Z= 0.335 Chirality : 0.045 0.174 611 Planarity : 0.007 0.059 683 Dihedral : 5.627 25.654 552 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.05 % Allowed : 18.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.40), residues: 480 helix: -5.41 (0.29), residues: 6 sheet: -2.03 (0.36), residues: 212 loop : -1.15 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 35 HIS 0.002 0.000 HIS L 55 PHE 0.031 0.002 PHE I 298 TYR 0.015 0.002 TYR H 51 ARG 0.006 0.001 ARG I 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.400 Fit side-chains REVERT: L 24 ARG cc_start: 0.6561 (mtp180) cc_final: 0.6214 (mtp-110) REVERT: I 297 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.5705 (pm20) REVERT: I 306 TRP cc_start: 0.7492 (m-90) cc_final: 0.7264 (m-90) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1687 time to fit residues: 10.6229 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.4227 r_free = 0.4227 target = 0.187737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153873 restraints weight = 4007.682| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.28 r_work: 0.3739 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3966 Z= 0.245 Angle : 0.630 7.449 5402 Z= 0.318 Chirality : 0.044 0.164 611 Planarity : 0.006 0.057 683 Dihedral : 5.406 24.985 552 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.51 % Allowed : 18.91 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.41), residues: 480 helix: -5.41 (0.29), residues: 6 sheet: -1.90 (0.36), residues: 213 loop : -0.99 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 PHE 0.036 0.002 PHE I 298 TYR 0.014 0.002 TYR I 249 ARG 0.007 0.000 ARG I 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.406 Fit side-chains REVERT: L 24 ARG cc_start: 0.6589 (mtp180) cc_final: 0.6213 (mtp-110) REVERT: I 250 ARG cc_start: 0.6456 (mtm-85) cc_final: 0.5879 (ttm-80) REVERT: I 297 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.5908 (pm20) REVERT: I 306 TRP cc_start: 0.7419 (m-90) cc_final: 0.7059 (m-90) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.1654 time to fit residues: 10.1084 Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain I residue 297 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.4243 r_free = 0.4243 target = 0.189457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155961 restraints weight = 3963.476| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.28 r_work: 0.3739 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3966 Z= 0.212 Angle : 0.603 6.848 5402 Z= 0.304 Chirality : 0.044 0.161 611 Planarity : 0.006 0.055 683 Dihedral : 5.167 24.584 552 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.96 % Allowed : 19.13 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.41), residues: 480 helix: -5.42 (0.28), residues: 6 sheet: -1.69 (0.37), residues: 213 loop : -0.89 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 PHE 0.035 0.002 PHE I 298 TYR 0.013 0.001 TYR I 249 ARG 0.005 0.000 ARG I 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.405 Fit side-chains REVERT: L 24 ARG cc_start: 0.6539 (mtp180) cc_final: 0.6175 (mtp-110) REVERT: I 295 GLN cc_start: 0.7031 (pt0) cc_final: 0.6750 (pt0) REVERT: I 297 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5671 (pm20) REVERT: I 306 TRP cc_start: 0.7308 (m-90) cc_final: 0.6897 (m-90) outliers start: 13 outliers final: 10 residues processed: 56 average time/residue: 0.1617 time to fit residues: 11.3558 Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151658 restraints weight = 4010.517| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.30 r_work: 0.3691 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 3966 Z= 0.318 Angle : 0.657 6.306 5402 Z= 0.331 Chirality : 0.045 0.161 611 Planarity : 0.006 0.055 683 Dihedral : 5.386 25.822 552 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.19 % Allowed : 18.45 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.42), residues: 480 helix: -5.45 (0.28), residues: 6 sheet: -1.74 (0.37), residues: 212 loop : -0.90 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 35 HIS 0.003 0.001 HIS L 55 PHE 0.038 0.003 PHE I 298 TYR 0.025 0.002 TYR L 87 ARG 0.007 0.001 ARG I 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.455 Fit side-chains REVERT: L 24 ARG cc_start: 0.6539 (mtp180) cc_final: 0.6157 (mtp-110) REVERT: I 250 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.6237 (mtm-85) REVERT: I 252 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6645 (ptp-170) REVERT: I 297 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.5713 (pm20) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.1629 time to fit residues: 11.1048 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.4239 r_free = 0.4239 target = 0.188942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.155125 restraints weight = 3995.983| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.30 r_work: 0.3736 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3966 Z= 0.231 Angle : 0.621 6.404 5402 Z= 0.312 Chirality : 0.044 0.159 611 Planarity : 0.006 0.055 683 Dihedral : 5.224 25.426 552 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.51 % Allowed : 20.05 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.94 (0.42), residues: 480 helix: -5.41 (0.29), residues: 6 sheet: -1.58 (0.37), residues: 212 loop : -0.79 (0.44), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP I 306 HIS 0.002 0.000 HIS L 55 PHE 0.037 0.002 PHE I 298 TYR 0.023 0.002 TYR L 87 ARG 0.006 0.001 ARG I 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.405 Fit side-chains REVERT: L 24 ARG cc_start: 0.6509 (mtp180) cc_final: 0.6142 (mtp-110) REVERT: I 250 ARG cc_start: 0.6432 (mtm-85) cc_final: 0.6223 (mtm-85) REVERT: I 295 GLN cc_start: 0.7055 (pt0) cc_final: 0.6776 (pt0) REVERT: I 297 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.5754 (pm20) outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.1782 time to fit residues: 11.8443 Evaluate side-chains 51 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.0020 chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.4244 r_free = 0.4244 target = 0.189455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155770 restraints weight = 3909.247| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.27 r_work: 0.3739 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3966 Z= 0.227 Angle : 0.615 6.539 5402 Z= 0.309 Chirality : 0.044 0.157 611 Planarity : 0.006 0.055 683 Dihedral : 5.136 24.937 552 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.51 % Allowed : 20.05 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.86 (0.42), residues: 480 helix: -5.39 (0.29), residues: 6 sheet: -1.45 (0.38), residues: 211 loop : -0.82 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP I 306 HIS 0.002 0.000 HIS L 55 PHE 0.036 0.002 PHE I 298 TYR 0.013 0.001 TYR I 249 ARG 0.006 0.001 ARG I 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.97 seconds wall clock time: 42 minutes 56.35 seconds (2576.35 seconds total)