Starting phenix.real_space_refine on Tue Jan 14 12:35:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8s_43044/01_2025/8v8s_43044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8s_43044/01_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_43044/01_2025/8v8s_43044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8s_43044/01_2025/8v8s_43044.map" model { file = "/net/cci-nas-00/data/ceres_data/8v8s_43044/01_2025/8v8s_43044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8s_43044/01_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-5571/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: 3.72, per 1000 atoms: 0.55 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: 1.66 Conformation dependent library (CDL) restraints added in 959.0 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: 0.48 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: 1.87 Time building geometry restraints manager: 1.93 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: 1.010 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.740 Find NCS groups from input model: 0.140 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:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- 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 : 0.707 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: 0.9251 time to fit residues: 138.3184 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 : 0.648 ------------------------------------------------------------------------------- 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 = 0.258351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.242570 restraints weight = 6269.177| |-----------------------------------------------------------------------------| 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: 0.5244 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.726 Fit side-chains REVERT: A 108 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7353 (mpt90) REVERT: B 108 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7351 (mpt90) REVERT: C 108 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7363 (mpt90) REVERT: D 108 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7351 (mpt90) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 1.3792 time to fit residues: 177.2000 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 : 0.702 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.0050 chunk 84 optimal weight: 0.6980 overall best weight: 0.4972 ------------------------------------------------------------------------------- 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 = 0.5525 r_free = 0.5525 target = 0.272521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.251892 restraints weight = 6586.491| |-----------------------------------------------------------------------------| r_work (start): 0.5412 rms_B_bonded: 1.57 r_work: 0.5407 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.5302 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.5302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2603 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= 0.154 Angle : 0.529 6.688 9268 Z= 0.276 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.033 1132 Dihedral : 3.940 19.352 924 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 11.21 % 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: 1.97 (0.28), residues: 884 helix: 1.89 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 PHE 0.007 0.001 PHE D 168 TYR 0.006 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 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.653 Fit side-chains REVERT: A 108 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7192 (mpt90) REVERT: B 108 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7170 (mpt90) REVERT: C 108 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7186 (mpt90) REVERT: D 108 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7198 (mpt90) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 1.1971 time to fit residues: 167.6462 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.5523 r_free = 0.5523 target = 0.272465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5484 r_free = 0.5484 target = 0.251198 restraints weight = 6659.814| |-----------------------------------------------------------------------------| r_work (start): 0.5409 rms_B_bonded: 1.57 r_work: 0.5409 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.5304 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.5304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6788 Z= 0.169 Angle : 0.535 6.543 9268 Z= 0.278 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.034 1132 Dihedral : 3.987 20.549 924 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.02 % Allowed : 10.63 % Favored : 85.34 % 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: 2.07 (0.28), residues: 884 helix: 1.98 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.003 0.001 HIS D 201 PHE 0.006 0.001 PHE C 218 TYR 0.007 0.001 TYR A 233 ARG 0.002 0.000 ARG C 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 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.690 Fit side-chains REVERT: A 108 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7446 (mtm-85) REVERT: B 108 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7205 (mpt90) REVERT: C 108 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7216 (mpt90) REVERT: D 108 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7445 (mtm-85) outliers start: 28 outliers final: 16 residues processed: 124 average time/residue: 1.1048 time to fit residues: 144.8212 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 : 0.716 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- 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: 0.5980 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 C 86 GLN D 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5490 r_free = 0.5490 target = 0.263789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.247694 restraints weight = 6289.882| |-----------------------------------------------------------------------------| r_work (start): 0.5404 rms_B_bonded: 1.64 r_work: 0.5399 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5289 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.5289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6788 Z= 0.171 Angle : 0.533 6.484 9268 Z= 0.277 Chirality : 0.040 0.108 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.997 20.901 924 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.02 % Allowed : 10.63 % Favored : 85.34 % 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: 2.11 (0.28), residues: 884 helix: 2.01 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.003 0.001 HIS C 201 PHE 0.006 0.001 PHE D 218 TYR 0.007 0.001 TYR B 233 ARG 0.002 0.000 ARG A 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 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.732 Fit side-chains REVERT: A 108 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7468 (mtm-85) REVERT: B 108 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7446 (mtm-85) REVERT: C 108 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7461 (mtm-85) REVERT: D 108 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7467 (mtm-85) outliers start: 28 outliers final: 16 residues processed: 119 average time/residue: 1.2392 time to fit residues: 155.3373 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 : 0.707 ------------------------------------------------------------------------------- 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: 0.0270 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.5523 r_free = 0.5523 target = 0.267532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.251745 restraints weight = 6296.240| |-----------------------------------------------------------------------------| r_work (start): 0.5439 rms_B_bonded: 1.63 r_work: 0.5434 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.5328 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.5328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2819 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= 0.142 Angle : 0.516 6.211 9268 Z= 0.266 Chirality : 0.039 0.108 1112 Planarity : 0.003 0.035 1132 Dihedral : 3.849 19.623 924 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.59 % Allowed : 13.07 % Favored : 84.34 % 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: 2.18 (0.28), residues: 884 helix: 2.09 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.06 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.002 0.000 HIS A 201 PHE 0.007 0.001 PHE D 168 TYR 0.006 0.001 TYR B 233 ARG 0.002 0.000 ARG C 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 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.710 Fit side-chains REVERT: A 108 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7439 (mtm-85) REVERT: B 108 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7428 (mtm-85) REVERT: C 108 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7460 (mtm-85) REVERT: D 108 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7449 (mtm-85) outliers start: 18 outliers final: 13 residues processed: 128 average time/residue: 1.1842 time to fit residues: 159.8917 Evaluate side-chains 129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.0470 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.5534 r_free = 0.5534 target = 0.272982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5495 r_free = 0.5495 target = 0.251682 restraints weight = 6568.900| |-----------------------------------------------------------------------------| r_work (start): 0.5423 rms_B_bonded: 1.56 r_work: 0.5422 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.5317 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.5317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6788 Z= 0.173 Angle : 0.540 6.430 9268 Z= 0.279 Chirality : 0.040 0.122 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.970 21.406 924 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.59 % Allowed : 14.37 % 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: 2.14 (0.28), residues: 884 helix: 2.07 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.04 (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 B 201 PHE 0.006 0.001 PHE B 168 TYR 0.007 0.001 TYR C 233 ARG 0.002 0.000 ARG B 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 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.840 Fit side-chains REVERT: A 108 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7265 (mpt180) REVERT: B 108 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7263 (mpt180) REVERT: C 108 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7273 (mpt180) REVERT: D 108 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7272 (mpt180) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 1.2024 time to fit residues: 151.0759 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 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 62 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.5528 r_free = 0.5528 target = 0.267680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5454 r_free = 0.5454 target = 0.251771 restraints weight = 6280.126| |-----------------------------------------------------------------------------| r_work (start): 0.5441 rms_B_bonded: 1.63 r_work: 0.5434 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.5327 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.5327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2849 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= 0.153 Angle : 0.538 6.174 9268 Z= 0.273 Chirality : 0.040 0.134 1112 Planarity : 0.003 0.035 1132 Dihedral : 3.878 20.509 924 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 13.07 % 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: 2.15 (0.28), residues: 884 helix: 2.11 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 35 HIS 0.002 0.000 HIS D 201 PHE 0.007 0.001 PHE D 168 TYR 0.006 0.001 TYR C 233 ARG 0.002 0.000 ARG A 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 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.678 Fit side-chains REVERT: A 108 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7273 (mpt180) REVERT: B 108 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7427 (mtm-85) REVERT: C 108 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7431 (mtm-85) REVERT: D 108 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7270 (mpt180) outliers start: 19 outliers final: 10 residues processed: 129 average time/residue: 1.1185 time to fit residues: 152.5664 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER 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 D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN D 201 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5496 r_free = 0.5496 target = 0.263613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5418 r_free = 0.5418 target = 0.247445 restraints weight = 6317.059| |-----------------------------------------------------------------------------| r_work (start): 0.5411 rms_B_bonded: 1.64 r_work: 0.5400 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.5290 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.5290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6788 Z= 0.189 Angle : 0.573 6.559 9268 Z= 0.292 Chirality : 0.041 0.120 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.013 21.658 924 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.30 % Allowed : 15.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 884 helix: 2.01 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.09 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.003 0.001 HIS A 201 PHE 0.008 0.001 PHE B 48 TYR 0.007 0.001 TYR B 233 ARG 0.002 0.001 ARG B 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 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.685 Fit side-chains REVERT: A 108 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7254 (mpt180) REVERT: B 108 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7261 (mpt180) REVERT: C 108 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7256 (mpt180) REVERT: D 108 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7261 (mpt180) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 1.2047 time to fit residues: 144.7100 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5478 r_free = 0.5478 target = 0.261812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5396 r_free = 0.5396 target = 0.245518 restraints weight = 6406.042| |-----------------------------------------------------------------------------| r_work (start): 0.5387 rms_B_bonded: 1.67 r_work: 0.5376 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.5266 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.5266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6788 Z= 0.216 Angle : 0.604 6.873 9268 Z= 0.308 Chirality : 0.042 0.117 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.149 22.492 924 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 15.23 % Favored : 82.47 % 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: 1.92 (0.28), residues: 884 helix: 1.94 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.13 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.003 0.001 HIS C 201 PHE 0.010 0.001 PHE B 48 TYR 0.009 0.001 TYR A 207 ARG 0.002 0.001 ARG A 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 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.725 Fit side-chains REVERT: A 108 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7313 (mpt180) REVERT: B 108 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7320 (mpt180) REVERT: C 108 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7326 (mpt180) REVERT: D 108 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7323 (mpt180) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 1.1977 time to fit residues: 141.3565 Evaluate side-chains 115 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 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 D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.0170 chunk 3 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.5526 r_free = 0.5526 target = 0.267329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5453 r_free = 0.5453 target = 0.251510 restraints weight = 6355.727| |-----------------------------------------------------------------------------| r_work (start): 0.5438 rms_B_bonded: 1.64 r_work: 0.5431 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5320 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.5320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6788 Z= 0.168 Angle : 0.577 6.931 9268 Z= 0.290 Chirality : 0.040 0.115 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.009 20.966 924 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.16 % Allowed : 15.66 % Favored : 82.18 % 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: 1.99 (0.28), residues: 884 helix: 1.97 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.09 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 35 HIS 0.002 0.000 HIS C 201 PHE 0.007 0.001 PHE D 168 TYR 0.007 0.001 TYR D 233 ARG 0.002 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5172.40 seconds wall clock time: 93 minutes 2.60 seconds (5582.60 seconds total)