Starting phenix.real_space_refine on Fri Dec 27 22:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzc_42839/12_2024/8uzc_42839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzc_42839/12_2024/8uzc_42839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uzc_42839/12_2024/8uzc_42839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzc_42839/12_2024/8uzc_42839.map" model { file = "/net/cci-nas-00/data/ceres_data/8uzc_42839/12_2024/8uzc_42839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzc_42839/12_2024/8uzc_42839.cif" } resolution = 3.8 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= -0.002 sd= 0.055 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2182 2.51 5 N 610 2.21 5 O 657 1.98 5 H 3367 0.53 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-5532/modules/chem_data/mon_lib" Total number of atoms: 6831 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1834 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1613 Classifications: {'peptide': 104} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3384 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain breaks: 2 Time building chain proxies: 3.88, per 1000 atoms: 0.57 Number of scatterers: 6831 At special positions: 0 Unit cell: (68.739, 79.154, 89.569, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 657 8.00 N 610 7.00 C 2182 6.00 H 3367 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 2.03 Conformation dependent library (CDL) restraints added in 707.9 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 9.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.721A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.535A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.355A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.518A pdb=" N THR A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.618A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.826A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AA5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.528A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 88 removed outlier: 5.641A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.555A pdb=" N LYS A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.555A pdb=" N LYS A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.611A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA A 138 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N SER A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 167 through 169 83 hydrogen bonds defined for protein. 189 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: 2.13 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3361 1.03 - 1.23: 33 1.23 - 1.43: 1515 1.43 - 1.62: 1982 1.62 - 1.82: 20 Bond restraints: 6911 Sorted by residual: bond pdb=" CA PHE H 52A" pdb=" C PHE H 52A" ideal model delta sigma weight residual 1.523 1.465 0.058 1.34e-02 5.57e+03 1.86e+01 bond pdb=" CA ASP H 53 " pdb=" C ASP H 53 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.40e-02 5.10e+03 1.79e+01 bond pdb=" CA SER H 55 " pdb=" C SER H 55 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.28e-02 6.10e+03 1.61e+01 bond pdb=" N GLN H 1 " pdb=" H3 GLN H 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 6906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12115 1.64 - 3.28: 246 3.28 - 4.92: 32 4.92 - 6.57: 2 6.57 - 8.21: 3 Bond angle restraints: 12398 Sorted by residual: angle pdb=" N SER H 55 " pdb=" CA SER H 55 " pdb=" C SER H 55 " ideal model delta sigma weight residual 112.94 107.37 5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" O SER H 52 " pdb=" C SER H 52 " pdb=" N PHE H 52A" ideal model delta sigma weight residual 122.03 125.58 -3.55 1.08e+00 8.57e-01 1.08e+01 angle pdb=" N ARG A 220 " pdb=" CA ARG A 220 " pdb=" C ARG A 220 " ideal model delta sigma weight residual 108.07 110.92 -2.85 8.90e-01 1.26e+00 1.03e+01 angle pdb=" N TYR H 100A" pdb=" CA TYR H 100A" pdb=" C TYR H 100A" ideal model delta sigma weight residual 114.75 110.72 4.03 1.26e+00 6.30e-01 1.02e+01 angle pdb=" N GLY H 10 " pdb=" CA GLY H 10 " pdb=" C GLY H 10 " ideal model delta sigma weight residual 110.20 114.40 -4.20 1.32e+00 5.74e-01 1.01e+01 ... (remaining 12393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2861 17.94 - 35.89: 337 35.89 - 53.83: 70 53.83 - 71.78: 17 71.78 - 89.72: 7 Dihedral angle restraints: 3292 sinusoidal: 1777 harmonic: 1515 Sorted by residual: dihedral pdb=" CA TRP A 153 " pdb=" C TRP A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 60.69 32.31 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA CYS A 64 " pdb=" C CYS A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 302 0.030 - 0.061: 148 0.061 - 0.091: 29 0.091 - 0.122: 33 0.122 - 0.152: 6 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 515 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 52 " 0.013 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C SER H 52 " -0.049 2.00e-02 2.50e+03 pdb=" O SER H 52 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE H 52A" 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 229 " 0.241 9.50e-02 1.11e+02 8.05e-02 7.13e+00 pdb=" NE ARG A 229 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 229 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 229 " 0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 229 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 229 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 229 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 229 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 55 " -0.014 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" N LYS H 56 " 0.044 2.00e-02 2.50e+03 pdb=" CA LYS H 56 " -0.011 2.00e-02 2.50e+03 pdb=" H LYS H 56 " -0.020 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 151 2.09 - 2.72: 11512 2.72 - 3.34: 19075 3.34 - 3.97: 24056 3.97 - 4.60: 37864 Nonbonded interactions: 92658 Sorted by model distance: nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.462 2.450 nonbonded pdb=" OE1 GLN H 105 " pdb=" H GLN H 105 " model vdw 1.586 2.450 nonbonded pdb=" OD1 ASP H 61 " pdb="HH22 ARG H 64 " model vdw 1.608 2.450 nonbonded pdb="HE21 GLN H 39 " pdb=" O LYS H 43 " model vdw 1.609 2.450 nonbonded pdb=" H TYR H 100F" pdb=" OH TYR L 36 " model vdw 1.647 2.450 ... (remaining 92653 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: 0.790 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 0.059 3544 Z= 0.269 Angle : 0.713 7.085 4803 Z= 0.412 Chirality : 0.044 0.152 518 Planarity : 0.006 0.107 618 Dihedral : 16.347 89.722 1287 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.02 % Rotamer: Outliers : 3.45 % Allowed : 20.95 % Favored : 75.60 % 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: -2.81 (0.39), residues: 431 helix: 0.22 (1.15), residues: 21 sheet: -2.36 (0.43), residues: 122 loop : -1.86 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.002 0.001 HIS A 184 PHE 0.011 0.001 PHE L 98 TYR 0.015 0.002 TYR L 92 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7179 (mmt) cc_final: 0.6412 (mmm) REVERT: L 85 VAL cc_start: 0.6119 (t) cc_final: 0.5911 (t) REVERT: A 58 ILE cc_start: 0.8002 (mm) cc_final: 0.7718 (pt) REVERT: A 154 LEU cc_start: 0.7755 (tp) cc_final: 0.7485 (mm) outliers start: 13 outliers final: 12 residues processed: 65 average time/residue: 0.3855 time to fit residues: 30.1090 Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3544 Z= 0.177 Angle : 0.598 5.215 4803 Z= 0.312 Chirality : 0.045 0.174 518 Planarity : 0.006 0.084 618 Dihedral : 7.855 59.638 509 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.12 % Favored : 91.65 % Rotamer: Outliers : 3.18 % Allowed : 20.95 % Favored : 75.86 % 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: -2.78 (0.38), residues: 431 helix: 0.99 (1.15), residues: 21 sheet: -2.28 (0.42), residues: 132 loop : -1.90 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE H 67 TYR 0.013 0.001 TYR L 49 ARG 0.002 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7625 (t) REVERT: L 4 MET cc_start: 0.7143 (mmt) cc_final: 0.6259 (mmm) REVERT: A 58 ILE cc_start: 0.7908 (mm) cc_final: 0.7678 (pt) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.3254 time to fit residues: 26.1130 Evaluate side-chains 61 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3544 Z= 0.198 Angle : 0.575 4.965 4803 Z= 0.301 Chirality : 0.045 0.170 518 Planarity : 0.006 0.071 618 Dihedral : 6.689 57.439 499 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.02 % Rotamer: Outliers : 3.45 % Allowed : 21.75 % Favored : 74.80 % 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: -2.80 (0.39), residues: 431 helix: 1.11 (1.19), residues: 21 sheet: -2.26 (0.42), residues: 134 loop : -1.94 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 94 HIS 0.002 0.001 HIS A 184 PHE 0.010 0.001 PHE L 98 TYR 0.013 0.002 TYR L 92 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7741 (t) REVERT: A 244 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6217 (tt) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.3381 time to fit residues: 26.6137 Evaluate side-chains 62 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3544 Z= 0.153 Angle : 0.535 4.846 4803 Z= 0.280 Chirality : 0.044 0.168 518 Planarity : 0.005 0.054 618 Dihedral : 6.481 55.478 499 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.45 % Allowed : 22.28 % Favored : 74.27 % 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: -2.63 (0.39), residues: 431 helix: 1.71 (1.19), residues: 21 sheet: -2.29 (0.42), residues: 138 loop : -1.76 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 103 HIS 0.002 0.000 HIS H 35 PHE 0.006 0.001 PHE L 98 TYR 0.014 0.001 TYR L 92 ARG 0.002 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8055 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 244 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6145 (tt) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.3970 time to fit residues: 31.3319 Evaluate side-chains 64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 89 GLN A 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3544 Z= 0.314 Angle : 0.631 5.183 4803 Z= 0.339 Chirality : 0.047 0.175 518 Planarity : 0.006 0.067 618 Dihedral : 6.901 53.132 499 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.15 % Favored : 85.85 % Rotamer: Outliers : 5.57 % Allowed : 20.16 % Favored : 74.27 % 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: -3.18 (0.37), residues: 431 helix: 0.43 (1.14), residues: 21 sheet: -2.44 (0.41), residues: 134 loop : -2.22 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 184 PHE 0.019 0.002 PHE L 98 TYR 0.024 0.002 TYR A 233 ARG 0.006 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7819 (t) REVERT: L 4 MET cc_start: 0.7132 (mmt) cc_final: 0.6556 (mmm) REVERT: L 6 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: A 244 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6356 (tt) outliers start: 21 outliers final: 17 residues processed: 65 average time/residue: 0.4055 time to fit residues: 31.4118 Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3544 Z= 0.186 Angle : 0.563 4.891 4803 Z= 0.297 Chirality : 0.045 0.170 518 Planarity : 0.005 0.055 618 Dihedral : 6.683 54.037 499 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 4.24 % Allowed : 20.69 % Favored : 75.07 % 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: -2.98 (0.38), residues: 431 helix: 0.98 (1.17), residues: 21 sheet: -2.38 (0.41), residues: 137 loop : -2.05 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 94 HIS 0.008 0.002 HIS A 156 PHE 0.009 0.001 PHE L 98 TYR 0.012 0.001 TYR H 91 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 71 LEU cc_start: 0.7329 (mp) cc_final: 0.7118 (mp) REVERT: A 244 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6335 (tt) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.3845 time to fit residues: 29.8863 Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3544 Z= 0.166 Angle : 0.551 5.601 4803 Z= 0.288 Chirality : 0.044 0.169 518 Planarity : 0.005 0.048 618 Dihedral : 6.413 53.896 499 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.24 % Allowed : 22.02 % Favored : 73.74 % 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: -2.80 (0.38), residues: 431 helix: 1.52 (1.17), residues: 21 sheet: -2.40 (0.42), residues: 131 loop : -1.91 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.004 0.001 HIS A 156 PHE 0.006 0.001 PHE L 98 TYR 0.011 0.001 TYR H 91 ARG 0.007 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6926 (mm) REVERT: H 62 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7745 (t) REVERT: A 244 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6283 (tt) outliers start: 16 outliers final: 11 residues processed: 62 average time/residue: 0.3484 time to fit residues: 26.6666 Evaluate side-chains 64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3544 Z= 0.196 Angle : 0.548 4.936 4803 Z= 0.288 Chirality : 0.044 0.171 518 Planarity : 0.009 0.185 618 Dihedral : 6.484 52.981 499 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 4.24 % Allowed : 22.02 % Favored : 73.74 % 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: -2.94 (0.38), residues: 431 helix: -0.10 (1.05), residues: 27 sheet: -2.40 (0.42), residues: 131 loop : -1.95 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE L 98 TYR 0.012 0.001 TYR H 91 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7785 (t) REVERT: A 244 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6410 (tt) outliers start: 16 outliers final: 13 residues processed: 62 average time/residue: 0.3291 time to fit residues: 25.9252 Evaluate side-chains 65 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3544 Z= 0.210 Angle : 0.559 4.945 4803 Z= 0.295 Chirality : 0.045 0.171 518 Planarity : 0.008 0.169 618 Dihedral : 6.262 51.519 497 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.98 % Allowed : 21.75 % Favored : 74.27 % 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: -2.97 (0.38), residues: 431 helix: -0.10 (1.04), residues: 27 sheet: -2.39 (0.42), residues: 131 loop : -2.01 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 94 HIS 0.002 0.001 HIS A 184 PHE 0.011 0.001 PHE L 98 TYR 0.012 0.001 TYR H 91 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7830 (t) REVERT: L 81 GLU cc_start: 0.6705 (mp0) cc_final: 0.6480 (mp0) REVERT: A 244 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6433 (tt) outliers start: 15 outliers final: 12 residues processed: 61 average time/residue: 0.3270 time to fit residues: 25.0554 Evaluate side-chains 64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3544 Z= 0.184 Angle : 0.549 4.893 4803 Z= 0.288 Chirality : 0.044 0.170 518 Planarity : 0.009 0.167 618 Dihedral : 6.186 50.841 497 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.98 % Allowed : 22.02 % Favored : 74.01 % 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: -2.92 (0.38), residues: 431 helix: 0.06 (1.06), residues: 27 sheet: -2.34 (0.42), residues: 131 loop : -1.99 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 94 HIS 0.001 0.001 HIS H 35 PHE 0.009 0.001 PHE L 98 TYR 0.012 0.001 TYR H 91 ARG 0.011 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 244 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6504 (tt) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.2743 time to fit residues: 20.3896 Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4219 r_free = 0.4219 target = 0.165746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149692 restraints weight = 15252.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.153739 restraints weight = 8660.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.156556 restraints weight = 5688.853| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3544 Z= 0.188 Angle : 0.544 4.901 4803 Z= 0.286 Chirality : 0.044 0.170 518 Planarity : 0.008 0.162 618 Dihedral : 6.163 51.314 497 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.98 % Allowed : 22.28 % Favored : 73.74 % 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: -2.91 (0.38), residues: 431 helix: 0.11 (1.06), residues: 27 sheet: -2.31 (0.42), residues: 131 loop : -2.00 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 94 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE L 98 TYR 0.013 0.001 TYR H 91 ARG 0.010 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.53 seconds wall clock time: 51 minutes 38.12 seconds (3098.12 seconds total)