Starting phenix.real_space_refine on Fri Jun 6 06:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8v_39060/06_2025/8y8v_39060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8v_39060/06_2025/8y8v_39060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8v_39060/06_2025/8y8v_39060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8v_39060/06_2025/8y8v_39060.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8v_39060/06_2025/8y8v_39060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8v_39060/06_2025/8y8v_39060.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.188 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 C 5072 2.51 5 N 1212 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 11, 'TRANS': 233} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'P5S:plan-3': 1, 'P5S:plan-1': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: C, B, D Time building chain proxies: 3.66, per 1000 atoms: 0.48 Number of scatterers: 7616 At special positions: 0 Unit cell: (85.425, 85.425, 65.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 4 15.00 O 1276 8.00 N 1212 7.00 C 5072 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: 1.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 33 through 61 Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.603A pdb=" N THR A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 167 through 190 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.515A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 244 through 253 removed outlier: 6.752A pdb=" N GLY A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 33 through 61 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.603A pdb=" N THR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 167 through 190 Processing helix chain 'B' and resid 201 through 218 removed outlier: 3.515A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 244 through 253 removed outlier: 6.752A pdb=" N GLY B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 33 through 61 Processing helix chain 'C' and resid 66 through 86 removed outlier: 3.603A pdb=" N THR C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 167 through 190 Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.515A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 244 through 253 removed outlier: 6.752A pdb=" N GLY C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 33 through 61 Processing helix chain 'D' and resid 66 through 86 removed outlier: 3.603A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 167 through 190 Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.515A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 244 through 253 removed outlier: 6.752A pdb=" N GLY D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix 540 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1380 1.33 - 1.45: 2112 1.45 - 1.57: 4244 1.57 - 1.69: 8 1.69 - 1.81: 96 Bond restraints: 7840 Sorted by residual: bond pdb=" N MET A 219 " pdb=" CA MET A 219 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.33e-02 5.65e+03 1.51e+00 bond pdb=" N MET C 219 " pdb=" CA MET C 219 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.33e-02 5.65e+03 1.51e+00 bond pdb=" N MET B 219 " pdb=" CA MET B 219 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.33e-02 5.65e+03 1.51e+00 bond pdb=" N MET D 219 " pdb=" CA MET D 219 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.33e-02 5.65e+03 1.51e+00 bond pdb=" C17 P5S B 500 " pdb=" O19 P5S B 500 " ideal model delta sigma weight residual 1.351 1.327 0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 7835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 10432 1.44 - 2.87: 148 2.87 - 4.31: 56 4.31 - 5.74: 20 5.74 - 7.17: 8 Bond angle restraints: 10664 Sorted by residual: angle pdb=" CA TYR D 223 " pdb=" CB TYR D 223 " pdb=" CG TYR D 223 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" CA TYR A 223 " pdb=" CB TYR A 223 " pdb=" CG TYR A 223 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " pdb=" CG TYR C 223 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" CA TYR B 223 " pdb=" CB TYR B 223 " pdb=" CG TYR B 223 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" C GLY A 218 " pdb=" N MET A 219 " pdb=" CA MET A 219 " ideal model delta sigma weight residual 122.06 117.40 4.66 1.86e+00 2.89e-01 6.28e+00 ... (remaining 10659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.01: 4108 27.01 - 54.01: 240 54.01 - 81.02: 32 81.02 - 108.02: 20 108.02 - 135.03: 8 Dihedral angle restraints: 4408 sinusoidal: 1680 harmonic: 2728 Sorted by residual: dihedral pdb=" C27 P5S D 500 " pdb=" C28 P5S D 500 " pdb=" C29 P5S D 500 " pdb=" C30 P5S D 500 " ideal model delta sinusoidal sigma weight residual 298.90 163.87 135.03 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C27 P5S A 500 " pdb=" C28 P5S A 500 " pdb=" C29 P5S A 500 " pdb=" C30 P5S A 500 " ideal model delta sinusoidal sigma weight residual 298.90 163.87 135.03 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C27 P5S C 500 " pdb=" C28 P5S C 500 " pdb=" C29 P5S C 500 " pdb=" C30 P5S C 500 " ideal model delta sinusoidal sigma weight residual 298.90 163.87 135.03 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 724 0.029 - 0.058: 296 0.058 - 0.086: 120 0.086 - 0.115: 32 0.115 - 0.144: 8 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CA TYR B 223 " pdb=" N TYR B 223 " pdb=" C TYR B 223 " pdb=" CB TYR B 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA TYR D 223 " pdb=" N TYR D 223 " pdb=" C TYR D 223 " pdb=" CB TYR D 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA TYR C 223 " pdb=" N TYR C 223 " pdb=" C TYR C 223 " pdb=" CB TYR C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1177 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 232 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 233 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 232 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO C 233 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 232 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO D 233 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " -0.017 5.00e-02 4.00e+02 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1896 2.79 - 3.32: 7424 3.32 - 3.85: 13884 3.85 - 4.37: 16452 4.37 - 4.90: 28048 Nonbonded interactions: 67704 Sorted by model distance: nonbonded pdb=" OH TYR C 67 " pdb=" O GLY C 214 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR D 67 " pdb=" O GLY D 214 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR B 67 " pdb=" O GLY B 214 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR A 67 " pdb=" O GLY A 214 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLU D 175 " pdb=" OG1 THR D 221 " model vdw 2.343 3.040 ... (remaining 67699 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: 0.06 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: 0.120 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.680 Find NCS groups from input model: 0.170 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.003 0.038 7840 Z= 0.127 Angle : 0.548 7.175 10664 Z= 0.281 Chirality : 0.038 0.144 1180 Planarity : 0.004 0.030 1312 Dihedral : 19.024 135.029 2696 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 20.42 % Favored : 76.96 % 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: 1.41 (0.26), residues: 972 helix: 1.73 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 169 HIS 0.001 0.001 HIS C 57 PHE 0.005 0.001 PHE C 76 TYR 0.019 0.001 TYR B 223 ARG 0.001 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.19071 ( 540) hydrogen bonds : angle 6.91910 ( 1596) covalent geometry : bond 0.00269 ( 7840) covalent geometry : angle 0.54832 (10664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.901 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 1.6504 time to fit residues: 214.2825 Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 219 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127763 restraints weight = 7067.645| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.14 r_work: 0.3274 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7840 Z= 0.203 Angle : 0.627 6.099 10664 Z= 0.336 Chirality : 0.045 0.159 1180 Planarity : 0.005 0.034 1312 Dihedral : 16.619 132.409 1180 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.09 % Allowed : 18.46 % Favored : 79.45 % 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 (0.27), residues: 972 helix: 2.30 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 169 HIS 0.008 0.002 HIS A 57 PHE 0.017 0.002 PHE A 236 TYR 0.024 0.003 TYR D 223 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 540) hydrogen bonds : angle 4.84847 ( 1596) covalent geometry : bond 0.00483 ( 7840) covalent geometry : angle 0.62716 (10664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.870 Fit side-chains REVERT: A 36 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: B 36 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: C 36 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: D 36 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7672 (mt-10) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 1.4629 time to fit residues: 197.1040 Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 154 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.0060 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 85 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.135572 restraints weight = 7073.795| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.12 r_work: 0.3365 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 7840 Z= 0.106 Angle : 0.479 5.796 10664 Z= 0.258 Chirality : 0.038 0.134 1180 Planarity : 0.004 0.033 1312 Dihedral : 15.427 131.823 1164 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.57 % Allowed : 19.37 % Favored : 79.06 % 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: 2.71 (0.27), residues: 972 helix: 2.77 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -0.66 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.005 0.001 HIS C 57 PHE 0.006 0.001 PHE C 236 TYR 0.018 0.001 TYR C 223 ARG 0.001 0.000 ARG C 229 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 540) hydrogen bonds : angle 4.39199 ( 1596) covalent geometry : bond 0.00237 ( 7840) covalent geometry : angle 0.47891 (10664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.874 Fit side-chains REVERT: A 36 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: B 36 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: C 36 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: D 36 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7602 (mt-10) outliers start: 12 outliers final: 0 residues processed: 140 average time/residue: 1.4983 time to fit residues: 220.6355 Evaluate side-chains 140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain D residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN B 183 GLN C 183 GLN D 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132181 restraints weight = 7062.665| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.14 r_work: 0.3326 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7840 Z= 0.129 Angle : 0.530 6.067 10664 Z= 0.281 Chirality : 0.040 0.144 1180 Planarity : 0.004 0.035 1312 Dihedral : 15.251 126.786 1160 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.57 % Allowed : 19.90 % Favored : 78.53 % 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: 2.64 (0.27), residues: 972 helix: 2.70 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.004 0.001 HIS A 57 PHE 0.013 0.001 PHE A 236 TYR 0.022 0.002 TYR D 223 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 540) hydrogen bonds : angle 4.41750 ( 1596) covalent geometry : bond 0.00302 ( 7840) covalent geometry : angle 0.52969 (10664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.884 Fit side-chains REVERT: A 36 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: B 36 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: C 36 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: D 36 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7670 (mt-10) outliers start: 12 outliers final: 4 residues processed: 140 average time/residue: 1.5016 time to fit residues: 222.0914 Evaluate side-chains 140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN C 245 GLN D 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128575 restraints weight = 7149.259| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.17 r_work: 0.3281 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7840 Z= 0.191 Angle : 0.611 6.409 10664 Z= 0.324 Chirality : 0.044 0.158 1180 Planarity : 0.005 0.036 1312 Dihedral : 15.625 126.649 1160 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.05 % Allowed : 21.07 % Favored : 77.88 % 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: 2.35 (0.27), residues: 972 helix: 2.49 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -0.71 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.004 0.002 HIS D 57 PHE 0.017 0.002 PHE C 236 TYR 0.024 0.003 TYR D 223 ARG 0.002 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 540) hydrogen bonds : angle 4.57744 ( 1596) covalent geometry : bond 0.00459 ( 7840) covalent geometry : angle 0.61108 (10664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.880 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 128 average time/residue: 1.6284 time to fit residues: 218.3632 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 245 GLN B 165 HIS B 245 GLN C 245 GLN D 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133015 restraints weight = 7173.662| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.15 r_work: 0.3341 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7840 Z= 0.114 Angle : 0.505 6.105 10664 Z= 0.268 Chirality : 0.039 0.141 1180 Planarity : 0.004 0.035 1312 Dihedral : 14.595 120.542 1148 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.52 % Allowed : 21.47 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.27), residues: 972 helix: 2.74 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 169 HIS 0.004 0.001 HIS B 57 PHE 0.009 0.001 PHE C 236 TYR 0.019 0.001 TYR B 223 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 540) hydrogen bonds : angle 4.32551 ( 1596) covalent geometry : bond 0.00268 ( 7840) covalent geometry : angle 0.50539 (10664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.124 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 132 average time/residue: 1.6285 time to fit residues: 227.0465 Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain D residue 61 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN C 245 GLN D 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129733 restraints weight = 7213.596| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.16 r_work: 0.3298 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7840 Z= 0.164 Angle : 0.576 6.675 10664 Z= 0.306 Chirality : 0.042 0.152 1180 Planarity : 0.005 0.036 1312 Dihedral : 14.608 117.747 1148 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.96 % Allowed : 20.03 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.27), residues: 972 helix: 2.61 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -0.74 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS C 57 PHE 0.015 0.002 PHE A 236 TYR 0.023 0.002 TYR C 223 ARG 0.001 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 540) hydrogen bonds : angle 4.45592 ( 1596) covalent geometry : bond 0.00393 ( 7840) covalent geometry : angle 0.57646 (10664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.778 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 136 average time/residue: 1.2126 time to fit residues: 174.2161 Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 248 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN C 245 GLN D 165 HIS D 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128840 restraints weight = 7244.847| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.17 r_work: 0.3288 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7840 Z= 0.175 Angle : 0.597 7.108 10664 Z= 0.316 Chirality : 0.043 0.157 1180 Planarity : 0.005 0.037 1312 Dihedral : 14.484 114.902 1148 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.70 % Allowed : 20.29 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.27), residues: 972 helix: 2.48 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.003 0.001 HIS C 57 PHE 0.016 0.002 PHE C 236 TYR 0.022 0.002 TYR A 223 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 540) hydrogen bonds : angle 4.49446 ( 1596) covalent geometry : bond 0.00420 ( 7840) covalent geometry : angle 0.59730 (10664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.901 Fit side-chains REVERT: A 275 PHE cc_start: 0.7673 (m-10) cc_final: 0.7425 (m-80) REVERT: B 275 PHE cc_start: 0.7676 (m-10) cc_final: 0.7428 (m-80) REVERT: C 275 PHE cc_start: 0.7669 (m-10) cc_final: 0.7422 (m-80) REVERT: D 275 PHE cc_start: 0.7676 (m-10) cc_final: 0.7430 (m-80) outliers start: 13 outliers final: 13 residues processed: 136 average time/residue: 1.1974 time to fit residues: 172.4178 Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 248 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN C 165 HIS C 245 GLN D 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129996 restraints weight = 7338.896| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.17 r_work: 0.3305 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7840 Z= 0.143 Angle : 0.561 7.195 10664 Z= 0.295 Chirality : 0.041 0.152 1180 Planarity : 0.005 0.035 1312 Dihedral : 14.275 113.654 1148 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.70 % Allowed : 19.76 % Favored : 78.53 % 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: 2.54 (0.27), residues: 972 helix: 2.51 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.003 0.001 HIS D 57 PHE 0.013 0.001 PHE D 236 TYR 0.021 0.002 TYR B 223 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 540) hydrogen bonds : angle 4.41692 ( 1596) covalent geometry : bond 0.00341 ( 7840) covalent geometry : angle 0.56072 (10664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.790 Fit side-chains REVERT: A 36 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: A 275 PHE cc_start: 0.7660 (m-10) cc_final: 0.7414 (m-80) REVERT: B 36 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: B 275 PHE cc_start: 0.7666 (m-10) cc_final: 0.7417 (m-80) REVERT: C 36 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 275 PHE cc_start: 0.7660 (m-10) cc_final: 0.7418 (m-80) REVERT: D 36 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: D 275 PHE cc_start: 0.7665 (m-10) cc_final: 0.7423 (m-80) outliers start: 13 outliers final: 9 residues processed: 132 average time/residue: 1.2540 time to fit residues: 175.3069 Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN C 245 GLN D 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128152 restraints weight = 7311.764| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.17 r_work: 0.3276 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7840 Z= 0.193 Angle : 0.621 7.525 10664 Z= 0.328 Chirality : 0.044 0.160 1180 Planarity : 0.005 0.037 1312 Dihedral : 14.498 114.357 1148 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.23 % Allowed : 18.19 % Favored : 79.58 % 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: 2.32 (0.27), residues: 972 helix: 2.37 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -0.45 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.003 0.002 HIS A 140 PHE 0.017 0.002 PHE B 236 TYR 0.023 0.003 TYR D 161 ARG 0.001 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 540) hydrogen bonds : angle 4.52433 ( 1596) covalent geometry : bond 0.00466 ( 7840) covalent geometry : angle 0.62128 (10664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.788 Fit side-chains REVERT: A 36 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: A 275 PHE cc_start: 0.7690 (m-10) cc_final: 0.7466 (m-80) REVERT: B 36 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: B 275 PHE cc_start: 0.7699 (m-10) cc_final: 0.7474 (m-80) REVERT: C 36 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: C 275 PHE cc_start: 0.7693 (m-10) cc_final: 0.7471 (m-80) REVERT: D 36 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: D 275 PHE cc_start: 0.7696 (m-10) cc_final: 0.7474 (m-80) outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 1.2185 time to fit residues: 164.8708 Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 84 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN C 245 GLN D 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131632 restraints weight = 7216.198| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.15 r_work: 0.3327 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7840 Z= 0.125 Angle : 0.537 7.182 10664 Z= 0.282 Chirality : 0.040 0.147 1180 Planarity : 0.004 0.035 1312 Dihedral : 14.067 113.097 1148 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.31 % Allowed : 19.63 % Favored : 79.06 % 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: 2.75 (0.27), residues: 972 helix: 2.64 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 57 PHE 0.011 0.001 PHE A 236 TYR 0.019 0.002 TYR B 223 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 540) hydrogen bonds : angle 4.33749 ( 1596) covalent geometry : bond 0.00295 ( 7840) covalent geometry : angle 0.53692 (10664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.98 seconds wall clock time: 99 minutes 40.98 seconds (5980.98 seconds total)