Starting phenix.real_space_refine on Tue Mar 11 20:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8s_43044/03_2025/8v8s_43044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8s_43044/03_2025/8v8s_43044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v8s_43044/03_2025/8v8s_43044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8s_43044/03_2025/8v8s_43044.map" model { file = "/net/cci-nas-00/data/ceres_data/8v8s_43044/03_2025/8v8s_43044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8s_43044/03_2025/8v8s_43044.cif" } resolution = 2.2 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4368 2.51 5 N 1060 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6717 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Restraints were copied for chains: C, B, D Time building chain proxies: 3.43, per 1000 atoms: 0.51 Number of scatterers: 6717 At special positions: 0 Unit cell: (77.562, 77.562, 67.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1237 8.00 N 1060 7.00 C 4368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 894.6 milliseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.644A pdb=" N THR A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 213 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 231 through 251 Proline residue: A 237 - end of helix Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 178 Processing helix chain 'B' and resid 188 through 205 Processing helix chain 'B' and resid 213 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 231 through 251 Proline residue: B 237 - end of helix Processing helix chain 'C' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 178 Processing helix chain 'C' and resid 188 through 205 Processing helix chain 'C' and resid 213 through 225 Proline residue: C 220 - end of helix Processing helix chain 'C' and resid 231 through 251 Proline residue: C 237 - end of helix Processing helix chain 'D' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 111 through 137 removed outlier: 3.568A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 178 Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 213 through 225 Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 231 through 251 Proline residue: D 237 - end of helix 485 hydrogen bonds defined for protein. 1455 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: 1.92 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2016 1.34 - 1.46: 1641 1.46 - 1.58: 3051 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 6788 Sorted by residual: bond pdb=" N MET C 212 " pdb=" CA MET C 212 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.48e-02 4.57e+03 7.57e-01 bond pdb=" N MET D 212 " pdb=" CA MET D 212 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.48e-02 4.57e+03 7.55e-01 bond pdb=" N MET A 212 " pdb=" CA MET A 212 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.48e-02 4.57e+03 7.37e-01 bond pdb=" N MET B 212 " pdb=" CA MET B 212 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.48e-02 4.57e+03 7.37e-01 bond pdb=" CB ASN C 226 " pdb=" CG ASN C 226 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01 ... (remaining 6783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 9017 1.16 - 2.32: 187 2.32 - 3.48: 44 3.48 - 4.64: 8 4.64 - 5.80: 12 Bond angle restraints: 9268 Sorted by residual: angle pdb=" C SER C 211 " pdb=" N MET C 212 " pdb=" CA MET C 212 " ideal model delta sigma weight residual 122.61 125.79 -3.18 1.56e+00 4.11e-01 4.17e+00 angle pdb=" C SER D 211 " pdb=" N MET D 212 " pdb=" CA MET D 212 " ideal model delta sigma weight residual 122.61 125.78 -3.17 1.56e+00 4.11e-01 4.13e+00 angle pdb=" C TYR B 250 " pdb=" N VAL B 251 " pdb=" CA VAL B 251 " ideal model delta sigma weight residual 123.16 121.01 2.15 1.06e+00 8.90e-01 4.12e+00 angle pdb=" C SER A 211 " pdb=" N MET A 212 " pdb=" CA MET A 212 " ideal model delta sigma weight residual 122.61 125.77 -3.16 1.56e+00 4.11e-01 4.11e+00 angle pdb=" C TYR A 250 " pdb=" N VAL A 251 " pdb=" CA VAL A 251 " ideal model delta sigma weight residual 123.16 121.01 2.15 1.06e+00 8.90e-01 4.10e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 3215 11.10 - 22.19: 369 22.19 - 33.29: 124 33.29 - 44.39: 76 44.39 - 55.48: 48 Dihedral angle restraints: 3832 sinusoidal: 1344 harmonic: 2488 Sorted by residual: dihedral pdb=" CA PHE D 203 " pdb=" C PHE D 203 " pdb=" N ALA D 204 " pdb=" CA ALA D 204 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE A 203 " pdb=" C PHE A 203 " pdb=" N ALA A 204 " pdb=" CA ALA A 204 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" N ALA B 204 " pdb=" CA ALA B 204 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 598 0.023 - 0.046: 266 0.046 - 0.069: 173 0.069 - 0.092: 42 0.092 - 0.114: 33 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA PRO D 237 " pdb=" N PRO D 237 " pdb=" C PRO D 237 " pdb=" CB PRO D 237 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 chirality pdb=" CA MET C 212 " pdb=" N MET C 212 " pdb=" C MET C 212 " pdb=" CB MET C 212 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 1109 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 236 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 237 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 237 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 237 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 237 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 236 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO D 237 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 237 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 237 " -0.018 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 557 2.74 - 3.28: 7142 3.28 - 3.82: 12239 3.82 - 4.36: 14558 4.36 - 4.90: 24304 Nonbonded interactions: 58800 Sorted by model distance: nonbonded pdb=" O HOH A 407 " pdb=" O HOH A 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH B 407 " pdb=" O HOH B 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH C 407 " pdb=" O HOH C 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH D 407 " pdb=" O HOH D 419 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG C 108 " pdb=" OH TYR C 250 " model vdw 2.308 3.120 ... (remaining 58795 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.360 Find NCS groups from input model: 0.120 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.002 0.018 6788 Z= 0.114 Angle : 0.472 5.805 9268 Z= 0.246 Chirality : 0.037 0.114 1112 Planarity : 0.004 0.033 1132 Dihedral : 14.020 55.483 2256 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % 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: 0.33 (0.27), residues: 884 helix: 0.29 (0.21), residues: 584 sheet: None (None), residues: 0 loop : 0.40 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.002 0.001 HIS A 230 PHE 0.007 0.001 PHE C 168 TYR 0.004 0.001 TYR B 233 ARG 0.002 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6827 (mtm-85) REVERT: B 250 TYR cc_start: 0.8740 (m-10) cc_final: 0.8355 (m-80) REVERT: C 108 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.6821 (mtm-85) REVERT: C 250 TYR cc_start: 0.8738 (m-10) cc_final: 0.8357 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.8796 time to fit residues: 131.5085 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5445 r_free = 0.5445 target = 0.258343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.242561 restraints weight = 6268.471| |-----------------------------------------------------------------------------| r_work (start): 0.5358 rms_B_bonded: 1.63 r_work: 0.5350 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.5242 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.5242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6788 Z= 0.242 Angle : 0.603 7.657 9268 Z= 0.320 Chirality : 0.042 0.148 1112 Planarity : 0.005 0.033 1132 Dihedral : 4.197 21.009 924 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.87 % Allowed : 11.21 % Favored : 85.92 % 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: 1.45 (0.27), residues: 884 helix: 1.39 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.19 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.007 0.001 PHE B 48 TYR 0.008 0.002 TYR B 233 ARG 0.004 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.846 Fit side-chains REVERT: A 108 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7357 (mpt90) REVERT: B 108 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7353 (mpt90) REVERT: C 108 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7367 (mpt90) REVERT: D 108 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7353 (mpt90) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 1.0657 time to fit residues: 137.8695 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 85 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.0770 chunk 64 optimal weight: 0.0020 chunk 84 optimal weight: 2.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5546 r_free = 0.5546 target = 0.274978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5509 r_free = 0.5509 target = 0.254535 restraints weight = 6588.761| |-----------------------------------------------------------------------------| r_work (start): 0.5434 rms_B_bonded: 1.56 r_work: 0.5432 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.5329 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.5329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6788 Z= 0.137 Angle : 0.518 6.567 9268 Z= 0.269 Chirality : 0.039 0.108 1112 Planarity : 0.004 0.033 1132 Dihedral : 3.858 18.620 924 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.58 % Allowed : 12.36 % Favored : 86.06 % 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: 2.02 (0.28), residues: 884 helix: 1.94 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 35 HIS 0.001 0.000 HIS D 201 PHE 0.007 0.001 PHE D 168 TYR 0.005 0.001 TYR C 233 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.756 Fit side-chains REVERT: A 108 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7201 (mpt90) REVERT: B 108 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7171 (mpt90) REVERT: C 108 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7186 (mpt90) REVERT: D 108 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7198 (mpt90) outliers start: 11 outliers final: 8 residues processed: 129 average time/residue: 1.1089 time to fit residues: 151.0018 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5487 r_free = 0.5487 target = 0.268944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5446 r_free = 0.5446 target = 0.246429 restraints weight = 6694.761| |-----------------------------------------------------------------------------| r_work (start): 0.5363 rms_B_bonded: 1.56 r_work: 0.5359 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.5255 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.5255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6788 Z= 0.231 Angle : 0.574 6.894 9268 Z= 0.302 Chirality : 0.041 0.110 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.183 21.946 924 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.17 % Allowed : 10.78 % Favored : 85.06 % 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: 1.93 (0.28), residues: 884 helix: 1.84 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.14 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 35 HIS 0.004 0.001 HIS C 201 PHE 0.006 0.001 PHE B 48 TYR 0.009 0.001 TYR D 233 ARG 0.003 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.759 Fit side-chains REVERT: A 108 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7227 (mpt90) REVERT: B 108 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7266 (mpt180) REVERT: C 108 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7276 (mpt180) REVERT: D 108 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7489 (mtm-85) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 1.1044 time to fit residues: 147.0540 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 41 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.273684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5496 r_free = 0.5496 target = 0.252459 restraints weight = 6576.007| |-----------------------------------------------------------------------------| r_work (start): 0.5419 rms_B_bonded: 1.56 r_work: 0.5416 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.5311 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.5311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6788 Z= 0.155 Angle : 0.525 6.506 9268 Z= 0.273 Chirality : 0.039 0.108 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.990 20.374 924 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.45 % Allowed : 10.63 % Favored : 85.92 % 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: 2.09 (0.28), residues: 884 helix: 2.00 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.10 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 PHE 0.007 0.001 PHE D 168 TYR 0.007 0.001 TYR A 233 ARG 0.002 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.803 Fit side-chains REVERT: A 108 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7444 (mtm-85) REVERT: B 108 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7449 (mtm-85) REVERT: C 108 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7434 (mtm-85) REVERT: D 108 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7433 (mtm-85) outliers start: 24 outliers final: 16 residues processed: 120 average time/residue: 1.2230 time to fit residues: 154.6669 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5511 r_free = 0.5511 target = 0.270726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5470 r_free = 0.5470 target = 0.249364 restraints weight = 6566.002| |-----------------------------------------------------------------------------| r_work (start): 0.5396 rms_B_bonded: 1.55 r_work: 0.5395 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.5291 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.5291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6788 Z= 0.190 Angle : 0.548 6.547 9268 Z= 0.286 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.076 21.698 924 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.59 % Allowed : 13.22 % Favored : 84.20 % 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: 2.04 (0.28), residues: 884 helix: 1.98 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.05 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.003 0.001 HIS A 201 PHE 0.006 0.001 PHE B 218 TYR 0.008 0.001 TYR A 233 ARG 0.002 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.728 Fit side-chains REVERT: A 108 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7469 (mtm180) REVERT: B 108 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: C 108 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7468 (mtm-85) REVERT: D 108 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7464 (mtm-85) outliers start: 18 outliers final: 16 residues processed: 116 average time/residue: 1.1379 time to fit residues: 139.3290 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5473 r_free = 0.5473 target = 0.261699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5394 r_free = 0.5394 target = 0.245484 restraints weight = 6275.937| |-----------------------------------------------------------------------------| r_work (start): 0.5387 rms_B_bonded: 1.64 r_work: 0.5380 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5271 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.5271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6788 Z= 0.196 Angle : 0.558 6.487 9268 Z= 0.290 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.115 22.107 924 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.87 % Allowed : 13.51 % Favored : 83.62 % 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: 2.04 (0.28), residues: 884 helix: 1.98 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.02 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.003 0.001 HIS A 201 PHE 0.006 0.001 PHE C 48 TYR 0.008 0.001 TYR B 233 ARG 0.002 0.001 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.710 Fit side-chains REVERT: A 108 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7484 (mtm180) REVERT: B 108 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7445 (mtm-85) REVERT: C 96 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6995 (mp) REVERT: C 108 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7482 (mtm-85) REVERT: D 108 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7456 (mtm-85) outliers start: 20 outliers final: 16 residues processed: 117 average time/residue: 1.1724 time to fit residues: 144.7473 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN D 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.262074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5398 r_free = 0.5398 target = 0.245881 restraints weight = 6266.963| |-----------------------------------------------------------------------------| r_work (start): 0.5391 rms_B_bonded: 1.64 r_work: 0.5383 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5273 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.5273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6788 Z= 0.195 Angle : 0.564 6.499 9268 Z= 0.292 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.118 21.879 924 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.02 % Allowed : 13.65 % Favored : 83.33 % 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: 2.02 (0.28), residues: 884 helix: 1.98 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.006 0.001 PHE C 218 TYR 0.008 0.001 TYR B 233 ARG 0.002 0.001 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.678 Fit side-chains REVERT: A 108 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7468 (mtm180) REVERT: B 108 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7441 (mtm-85) REVERT: C 96 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6994 (mp) REVERT: C 108 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: D 108 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7456 (mtm-85) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 1.1208 time to fit residues: 138.4020 Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 0.0010 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.272863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5495 r_free = 0.5495 target = 0.252295 restraints weight = 6585.412| |-----------------------------------------------------------------------------| r_work (start): 0.5423 rms_B_bonded: 1.56 r_work: 0.5417 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.5314 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.5314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6788 Z= 0.166 Angle : 0.554 6.307 9268 Z= 0.283 Chirality : 0.040 0.110 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.027 21.167 924 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.45 % Allowed : 13.07 % Favored : 83.48 % 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: 2.05 (0.28), residues: 884 helix: 2.02 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.05 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 35 HIS 0.002 0.001 HIS D 201 PHE 0.007 0.001 PHE C 168 TYR 0.007 0.001 TYR A 233 ARG 0.002 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.738 Fit side-chains REVERT: A 108 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7221 (mpt180) REVERT: B 108 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7436 (mtm-85) REVERT: C 108 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7434 (mtm-85) REVERT: D 108 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7448 (mtm-85) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 1.0838 time to fit residues: 142.3244 Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN D 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5472 r_free = 0.5472 target = 0.261597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5390 r_free = 0.5390 target = 0.245243 restraints weight = 6416.606| |-----------------------------------------------------------------------------| r_work (start): 0.5384 rms_B_bonded: 1.67 r_work: 0.5371 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.5259 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.5259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6788 Z= 0.212 Angle : 0.607 6.489 9268 Z= 0.309 Chirality : 0.042 0.144 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.176 22.550 924 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.87 % Allowed : 14.08 % Favored : 83.05 % 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: 1.93 (0.28), residues: 884 helix: 1.94 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.003 0.001 HIS A 201 PHE 0.009 0.001 PHE B 48 TYR 0.009 0.001 TYR A 207 ARG 0.002 0.001 ARG C 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.718 Fit side-chains REVERT: A 108 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7330 (mpt180) REVERT: B 108 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7447 (mtm-85) REVERT: C 108 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: D 108 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7474 (mtm-85) outliers start: 20 outliers final: 16 residues processed: 112 average time/residue: 1.1846 time to fit residues: 139.9147 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 0.0470 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5517 r_free = 0.5517 target = 0.266747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5444 r_free = 0.5444 target = 0.250823 restraints weight = 6362.486| |-----------------------------------------------------------------------------| r_work (start): 0.5389 rms_B_bonded: 1.65 r_work: 0.5348 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.5229 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.5229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6788 Z= 0.166 Angle : 0.575 6.291 9268 Z= 0.290 Chirality : 0.040 0.131 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.005 20.915 924 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 14.37 % Favored : 82.76 % 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 (0.28), residues: 884 helix: 2.03 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.19 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.002 0.001 HIS B 201 PHE 0.007 0.001 PHE B 168 TYR 0.007 0.001 TYR D 233 ARG 0.002 0.000 ARG D 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5173.53 seconds wall clock time: 89 minutes 1.08 seconds (5341.08 seconds total)