Starting phenix.real_space_refine on Wed Mar 5 17:17:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bee_44477/03_2025/9bee_44477_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bee_44477/03_2025/9bee_44477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bee_44477/03_2025/9bee_44477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bee_44477/03_2025/9bee_44477.map" model { file = "/net/cci-nas-00/data/ceres_data/9bee_44477/03_2025/9bee_44477_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bee_44477/03_2025/9bee_44477_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 1 5.16 5 C 962 2.51 5 N 285 2.21 5 O 297 1.98 5 H 1501 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3046 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1408 Classifications: {'peptide': 88} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "A" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1638 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.26, per 1000 atoms: 0.74 Number of scatterers: 3046 At special positions: 0 Unit cell: (78.012, 43.34, 107.956, 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 1 16.00 O 297 8.00 N 285 7.00 C 962 6.00 H 1501 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 196.3 milliseconds 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 366 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 4 sheets defined 1.6% alpha, 49.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing sheet with id=AA1, first strand: chain 'B' and resid 77 through 80 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.869A pdb=" N PHE B 113 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 113 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 116 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU A 105 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 118 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS A 103 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG A 120 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS A 101 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR A 122 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU A 99 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.517A pdb=" N VAL A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 162 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: 1.22 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 844 1.04 - 1.23: 739 1.23 - 1.42: 562 1.42 - 1.62: 927 1.62 - 1.81: 2 Bond restraints: 3074 Sorted by residual: bond pdb=" N ARG B 116 " pdb=" H ARG B 116 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 143 " pdb=" H LEU B 143 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 TYR B 122 " pdb=" HD2 TYR B 122 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ILE B 159 " pdb=" H ILE B 159 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N SER B 135 " pdb=" H SER B 135 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 3069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 3823 1.60 - 3.20: 1311 3.20 - 4.80: 295 4.80 - 6.41: 91 6.41 - 8.01: 38 Bond angle restraints: 5558 Sorted by residual: angle pdb=" CA ARG A 116 " pdb=" C ARG A 116 " pdb=" O ARG A 116 " ideal model delta sigma weight residual 121.06 115.75 5.31 1.16e+00 7.43e-01 2.09e+01 angle pdb=" CA GLY A 154 " pdb=" C GLY A 154 " pdb=" O GLY A 154 " ideal model delta sigma weight residual 122.46 118.24 4.22 9.70e-01 1.06e+00 1.89e+01 angle pdb=" CA VAL A 97 " pdb=" C VAL A 97 " pdb=" O VAL A 97 " ideal model delta sigma weight residual 121.63 117.64 3.99 9.90e-01 1.02e+00 1.63e+01 angle pdb=" N ARG A 116 " pdb=" CA ARG A 116 " pdb=" CB ARG A 116 " ideal model delta sigma weight residual 111.53 104.26 7.27 1.86e+00 2.89e-01 1.53e+01 angle pdb=" N ASN B 146 " pdb=" CA ASN B 146 " pdb=" CB ASN B 146 " ideal model delta sigma weight residual 111.55 104.91 6.64 1.74e+00 3.30e-01 1.46e+01 ... (remaining 5553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 1297 15.55 - 31.10: 86 31.10 - 46.65: 25 46.65 - 62.19: 22 62.19 - 77.74: 12 Dihedral angle restraints: 1442 sinusoidal: 803 harmonic: 639 Sorted by residual: dihedral pdb=" C GLU B 156 " pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta harmonic sigma weight residual -122.60 -132.55 9.95 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta harmonic sigma weight residual 122.80 131.93 -9.13 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C VAL B 142 " pdb=" N VAL B 142 " pdb=" CA VAL B 142 " pdb=" CB VAL B 142 " ideal model delta harmonic sigma weight residual -122.00 -129.65 7.65 0 2.50e+00 1.60e-01 9.36e+00 ... (remaining 1439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 123 0.067 - 0.135: 72 0.135 - 0.202: 37 0.202 - 0.270: 7 0.270 - 0.337: 1 Chirality restraints: 240 Sorted by residual: chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA PRO A 86 " pdb=" N PRO A 86 " pdb=" C PRO A 86 " pdb=" CB PRO A 86 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA UNK A 26 " pdb=" N UNK A 26 " pdb=" C UNK A 26 " pdb=" CB UNK A 26 " both_signs ideal model delta sigma weight residual False 2.52 2.27 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 237 not shown) Planarity restraints: 453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 116 " -0.030 9.50e-02 1.11e+02 6.55e-02 9.43e+01 pdb=" NE ARG B 116 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 116 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 116 " -0.101 2.00e-02 2.50e+03 pdb=" NH2 ARG B 116 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG B 116 " -0.042 2.00e-02 2.50e+03 pdb="HH12 ARG B 116 " 0.136 2.00e-02 2.50e+03 pdb="HH21 ARG B 116 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG B 116 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 107 " 0.024 9.50e-02 1.11e+02 5.15e-02 5.82e+01 pdb=" NE ARG B 107 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 107 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 107 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG B 107 " 0.028 2.00e-02 2.50e+03 pdb="HH11 ARG B 107 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 107 " 0.077 2.00e-02 2.50e+03 pdb="HH21 ARG B 107 " 0.067 2.00e-02 2.50e+03 pdb="HH22 ARG B 107 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 146 " 0.056 2.00e-02 2.50e+03 6.03e-02 5.45e+01 pdb=" CG ASN A 146 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 146 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN A 146 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 146 " 0.089 2.00e-02 2.50e+03 pdb="HD22 ASN A 146 " -0.087 2.00e-02 2.50e+03 ... (remaining 450 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 224 2.22 - 2.81: 5994 2.81 - 3.41: 7524 3.41 - 4.00: 9812 4.00 - 4.60: 14142 Nonbonded interactions: 37696 Sorted by model distance: nonbonded pdb=" HG SER A 85 " pdb=" OE1 GLU A 88 " model vdw 1.620 2.450 nonbonded pdb=" OD1 ASN B 78 " pdb=" HG1 THR B 144 " model vdw 1.691 2.450 nonbonded pdb=" O VAL B 81 " pdb=" H PHE B 84 " model vdw 1.698 2.450 nonbonded pdb=" OE1 GLU B 99 " pdb=" HZ3 LYS B 121 " model vdw 1.763 2.450 nonbonded pdb=" OE1 GLU A 87 " pdb=" H GLU A 87 " model vdw 1.792 2.450 ... (remaining 37691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 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 : 0.013 0.047 1573 Z= 0.887 Angle : 1.844 7.267 2123 Z= 1.233 Chirality : 0.098 0.337 240 Planarity : 0.016 0.100 280 Dihedral : 11.725 76.567 605 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Cbeta Deviations : 0.55 % 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: -2.32 (0.60), residues: 185 helix: None (None), residues: 0 sheet: -1.28 (0.58), residues: 77 loop : -1.75 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS B 83 PHE 0.042 0.012 PHE B 84 TYR 0.081 0.020 TYR B 122 ARG 0.009 0.002 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8799 (mp0) cc_final: 0.8515 (mp0) REVERT: A 67 GLU cc_start: 0.4546 (mm-30) cc_final: 0.3567 (pt0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3927 time to fit residues: 28.9564 Evaluate side-chains 48 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.171662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141442 restraints weight = 7120.884| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 4.62 r_work: 0.3913 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1573 Z= 0.191 Angle : 0.632 4.677 2123 Z= 0.328 Chirality : 0.049 0.168 240 Planarity : 0.004 0.028 280 Dihedral : 4.120 14.789 212 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % Favored : 83.91 % 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: -2.00 (0.61), residues: 185 helix: None (None), residues: 0 sheet: -1.27 (0.50), residues: 95 loop : -1.26 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 119 PHE 0.018 0.002 PHE A 75 TYR 0.006 0.002 TYR A 122 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8902 (mp0) cc_final: 0.8539 (mp0) REVERT: A 67 GLU cc_start: 0.4583 (mm-30) cc_final: 0.3629 (pt0) REVERT: A 132 THR cc_start: 0.8238 (t) cc_final: 0.7986 (p) outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.3336 time to fit residues: 20.9165 Evaluate side-chains 51 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.168798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.139788 restraints weight = 7220.653| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 4.54 r_work: 0.3898 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1573 Z= 0.166 Angle : 0.549 3.980 2123 Z= 0.286 Chirality : 0.048 0.162 240 Planarity : 0.004 0.036 280 Dihedral : 3.914 12.838 212 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.15 % Allowed : 18.97 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.66), residues: 185 helix: None (None), residues: 0 sheet: -0.87 (0.51), residues: 101 loop : -0.66 (0.80), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 119 PHE 0.011 0.002 PHE A 75 TYR 0.006 0.002 TYR B 122 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6684 (t-90) REVERT: B 110 GLU cc_start: 0.8917 (mp0) cc_final: 0.8541 (mp0) REVERT: A 67 GLU cc_start: 0.4851 (mm-30) cc_final: 0.3718 (pt0) REVERT: A 132 THR cc_start: 0.8194 (t) cc_final: 0.7895 (p) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.3244 time to fit residues: 18.6413 Evaluate side-chains 46 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain A residue 113 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.166687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.137267 restraints weight = 7312.433| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 4.56 r_work: 0.3872 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1573 Z= 0.145 Angle : 0.515 3.896 2123 Z= 0.265 Chirality : 0.048 0.156 240 Planarity : 0.004 0.028 280 Dihedral : 3.814 13.028 212 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.02 % Allowed : 15.52 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.68), residues: 185 helix: None (None), residues: 0 sheet: -0.66 (0.52), residues: 101 loop : -0.37 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 111 PHE 0.011 0.002 PHE A 75 TYR 0.006 0.002 TYR B 122 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8924 (mp0) cc_final: 0.8539 (mp0) REVERT: B 156 GLU cc_start: 0.7785 (mp0) cc_final: 0.7175 (mp0) REVERT: A 68 MET cc_start: 0.7285 (mtt) cc_final: 0.6826 (mtp) REVERT: A 132 THR cc_start: 0.8219 (t) cc_final: 0.7951 (p) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.3787 time to fit residues: 20.2550 Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.164905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.134067 restraints weight = 7303.652| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.72 r_work: 0.3834 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1573 Z= 0.150 Angle : 0.499 3.676 2123 Z= 0.257 Chirality : 0.047 0.156 240 Planarity : 0.005 0.044 280 Dihedral : 3.744 12.920 212 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.87 % Allowed : 18.39 % Favored : 78.74 % 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: -0.84 (0.68), residues: 185 helix: None (None), residues: 0 sheet: -0.58 (0.52), residues: 101 loop : -0.32 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 111 PHE 0.011 0.002 PHE A 75 TYR 0.005 0.002 TYR B 122 ARG 0.005 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.238 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: B 110 GLU cc_start: 0.8980 (mp0) cc_final: 0.8613 (mp0) REVERT: B 156 GLU cc_start: 0.7800 (mp0) cc_final: 0.7160 (mp0) REVERT: A 68 MET cc_start: 0.7433 (mtt) cc_final: 0.7005 (mtp) REVERT: A 108 GLN cc_start: 0.8631 (tp40) cc_final: 0.8268 (tm-30) REVERT: A 132 THR cc_start: 0.8273 (t) cc_final: 0.7854 (p) outliers start: 5 outliers final: 5 residues processed: 52 average time/residue: 0.3476 time to fit residues: 19.9026 Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.164424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133423 restraints weight = 7427.478| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.75 r_work: 0.3826 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1573 Z= 0.144 Angle : 0.502 3.669 2123 Z= 0.257 Chirality : 0.047 0.155 240 Planarity : 0.005 0.045 280 Dihedral : 3.688 12.904 212 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.45 % Allowed : 19.54 % Favored : 77.01 % 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: -0.73 (0.68), residues: 185 helix: None (None), residues: 0 sheet: -0.49 (0.52), residues: 101 loop : -0.27 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 111 PHE 0.012 0.002 PHE A 75 TYR 0.005 0.001 TYR B 122 ARG 0.005 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8993 (mp0) cc_final: 0.8628 (mp0) REVERT: B 156 GLU cc_start: 0.7819 (mp0) cc_final: 0.7162 (mp0) REVERT: A 68 MET cc_start: 0.7428 (mtt) cc_final: 0.7000 (mtp) REVERT: A 108 GLN cc_start: 0.8564 (tp40) cc_final: 0.8226 (mm110) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.3923 time to fit residues: 21.3278 Evaluate side-chains 48 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.163694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134050 restraints weight = 7339.073| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 4.64 r_work: 0.3837 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1573 Z= 0.137 Angle : 0.489 3.666 2123 Z= 0.251 Chirality : 0.047 0.154 240 Planarity : 0.005 0.052 280 Dihedral : 3.609 12.377 212 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.02 % Allowed : 19.54 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.66), residues: 185 helix: None (None), residues: 0 sheet: -0.33 (0.53), residues: 99 loop : -0.42 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 119 PHE 0.012 0.002 PHE A 75 TYR 0.006 0.002 TYR B 122 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.9012 (mp0) cc_final: 0.8655 (mp0) REVERT: B 156 GLU cc_start: 0.7855 (mp0) cc_final: 0.7193 (mp0) REVERT: A 68 MET cc_start: 0.7447 (mtt) cc_final: 0.7040 (mtp) REVERT: A 108 GLN cc_start: 0.8527 (tp40) cc_final: 0.8213 (tm-30) outliers start: 7 outliers final: 6 residues processed: 50 average time/residue: 0.3000 time to fit residues: 16.6960 Evaluate side-chains 51 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.164281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.134355 restraints weight = 7207.622| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 4.67 r_work: 0.3841 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1573 Z= 0.136 Angle : 0.475 3.667 2123 Z= 0.244 Chirality : 0.047 0.150 240 Planarity : 0.005 0.057 280 Dihedral : 3.485 11.406 212 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.02 % Allowed : 20.69 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.65), residues: 185 helix: None (None), residues: 0 sheet: -0.01 (0.54), residues: 93 loop : -0.78 (0.72), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 119 PHE 0.014 0.002 PHE A 75 TYR 0.005 0.001 TYR B 122 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.258 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: B 110 GLU cc_start: 0.9004 (mp0) cc_final: 0.8642 (mp0) REVERT: B 156 GLU cc_start: 0.7852 (mp0) cc_final: 0.7170 (mp0) REVERT: A 68 MET cc_start: 0.7402 (mtt) cc_final: 0.6997 (mtp) REVERT: A 108 GLN cc_start: 0.8544 (tp40) cc_final: 0.8253 (mm110) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.3428 time to fit residues: 18.6446 Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131595 restraints weight = 7393.308| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 4.64 r_work: 0.3799 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1573 Z= 0.174 Angle : 0.512 3.713 2123 Z= 0.266 Chirality : 0.048 0.164 240 Planarity : 0.006 0.060 280 Dihedral : 3.793 13.763 212 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.45 % Allowed : 21.84 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.63), residues: 185 helix: None (None), residues: 0 sheet: -0.12 (0.53), residues: 93 loop : -0.97 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 111 PHE 0.013 0.003 PHE A 75 TYR 0.007 0.002 TYR B 122 ARG 0.009 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.9004 (mp0) cc_final: 0.8637 (mp0) REVERT: B 156 GLU cc_start: 0.7912 (mp0) cc_final: 0.7217 (mp0) REVERT: A 108 GLN cc_start: 0.8541 (tp40) cc_final: 0.8138 (mm-40) outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.3151 time to fit residues: 16.4693 Evaluate side-chains 47 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.163129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.133538 restraints weight = 7236.948| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 4.62 r_work: 0.3829 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1573 Z= 0.134 Angle : 0.490 3.743 2123 Z= 0.251 Chirality : 0.047 0.157 240 Planarity : 0.005 0.050 280 Dihedral : 3.584 11.736 212 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.45 % Allowed : 21.26 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.63), residues: 185 helix: None (None), residues: 0 sheet: 0.04 (0.53), residues: 93 loop : -0.93 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 119 PHE 0.013 0.002 PHE A 75 TYR 0.005 0.001 TYR B 122 ARG 0.006 0.000 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.9007 (mp0) cc_final: 0.8644 (mp0) REVERT: B 156 GLU cc_start: 0.7930 (mp0) cc_final: 0.7242 (mp0) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.3370 time to fit residues: 18.2715 Evaluate side-chains 48 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.162698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132559 restraints weight = 7393.542| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.77 r_work: 0.3814 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1573 Z= 0.138 Angle : 0.480 3.730 2123 Z= 0.246 Chirality : 0.047 0.155 240 Planarity : 0.004 0.039 280 Dihedral : 3.478 12.500 212 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.45 % Allowed : 20.11 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.63), residues: 185 helix: None (None), residues: 0 sheet: 0.34 (0.56), residues: 85 loop : -0.92 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 119 PHE 0.012 0.002 PHE A 75 TYR 0.005 0.002 TYR B 122 ARG 0.002 0.000 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.29 seconds wall clock time: 51 minutes 45.72 seconds (3105.72 seconds total)