Starting phenix.real_space_refine on Fri May 9 13:35:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y84_39032/05_2025/8y84_39032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y84_39032/05_2025/8y84_39032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y84_39032/05_2025/8y84_39032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y84_39032/05_2025/8y84_39032.map" model { file = "/net/cci-nas-00/data/ceres_data/8y84_39032/05_2025/8y84_39032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y84_39032/05_2025/8y84_39032.cif" } resolution = 2.98 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= 0.032 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 13 5.16 5 C 1453 2.51 5 N 330 2.21 5 O 372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2168 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 331 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1227 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 1, 'TRANS': 156} Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 1.07 Number of scatterers: 2168 At special positions: 0 Unit cell: (64.2, 68.48, 73.83, 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 13 16.00 O 372 8.00 N 330 7.00 C 1453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS G 25 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 260.0 milliseconds 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 88.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.568A pdb=" N LEU A 203 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 234 removed outlier: 3.546A pdb=" N SER A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 57 through 83 removed outlier: 4.277A pdb=" N GLN B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.747A pdb=" N LEU B 107 " --> pdb=" O TRP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 161 removed outlier: 4.176A pdb=" N TYR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 205 removed outlier: 3.553A pdb=" N PHE B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 removed outlier: 3.686A pdb=" N ARG C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 56 removed outlier: 3.708A pdb=" N LEU G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE G 48 " --> pdb=" O CYS G 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 543 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: 0.56 Time building geometry restraints manager: 0.69 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: 363 1.33 - 1.45: 558 1.45 - 1.57: 1273 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2210 Sorted by residual: bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta sigma weight residual 1.462 1.529 -0.067 1.46e-02 4.69e+03 2.11e+01 bond pdb=" C ILE A 198 " pdb=" N GLU A 199 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.45e-02 4.76e+03 6.28e+00 bond pdb=" CAX Y01 B 601 " pdb=" OAF Y01 B 601 " ideal model delta sigma weight residual 1.247 1.207 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C PHE A 207 " pdb=" N PRO A 208 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.90e+00 ... (remaining 2205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 2922 2.98 - 5.95: 57 5.95 - 8.93: 18 8.93 - 11.91: 2 11.91 - 14.88: 1 Bond angle restraints: 3000 Sorted by residual: angle pdb=" N ILE C 55 " pdb=" CA ILE C 55 " pdb=" C ILE C 55 " ideal model delta sigma weight residual 113.22 107.51 5.71 1.23e+00 6.61e-01 2.16e+01 angle pdb=" C VAL B 127 " pdb=" N ARG B 128 " pdb=" CA ARG B 128 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" CA LEU B 58 " pdb=" CB LEU B 58 " pdb=" CG LEU B 58 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " ideal model delta sigma weight residual 116.20 123.92 -7.72 2.00e+00 2.50e-01 1.49e+01 angle pdb=" O ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " ideal model delta sigma weight residual 123.00 117.35 5.65 1.60e+00 3.91e-01 1.25e+01 ... (remaining 2995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 1142 15.17 - 30.33: 151 30.33 - 45.49: 38 45.49 - 60.66: 14 60.66 - 75.82: 2 Dihedral angle restraints: 1347 sinusoidal: 564 harmonic: 783 Sorted by residual: dihedral pdb=" CB CYS C 25 " pdb=" SG CYS C 25 " pdb=" SG CYS G 25 " pdb=" CB CYS G 25 " ideal model delta sinusoidal sigma weight residual 93.00 147.37 -54.37 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA MET B 183 " pdb=" C MET B 183 " pdb=" N LEU B 184 " pdb=" CA LEU B 184 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLU A 199 " pdb=" C GLU A 199 " pdb=" N TYR A 200 " pdb=" CA TYR A 200 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 304 0.066 - 0.132: 51 0.132 - 0.198: 10 0.198 - 0.264: 4 0.264 - 0.330: 2 Chirality restraints: 371 Sorted by residual: chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.52 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CBD Y01 B 601 " pdb=" CAK Y01 B 601 " pdb=" CBF Y01 B 601 " pdb=" CBG Y01 B 601 " both_signs ideal model delta sigma weight residual False 2.70 2.93 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 368 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ILE A 198 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE A 198 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 101 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C PRO B 101 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO B 101 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE B 102 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 220 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLY A 220 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY A 220 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 221 " 0.014 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 539 2.80 - 3.32: 2149 3.32 - 3.85: 3728 3.85 - 4.37: 4323 4.37 - 4.90: 7381 Nonbonded interactions: 18120 Sorted by model distance: nonbonded pdb=" OH TYR C 35 " pdb=" OG1 THR G 40 " model vdw 2.269 3.040 nonbonded pdb=" O THR B 174 " pdb=" OG1 THR B 178 " model vdw 2.319 3.040 nonbonded pdb=" O VAL B 78 " pdb=" OG1 THR B 82 " model vdw 2.338 3.040 nonbonded pdb=" O LEU B 184 " pdb=" OG1 THR B 188 " model vdw 2.345 3.040 nonbonded pdb=" O GLY B 170 " pdb=" OG1 THR B 174 " model vdw 2.381 3.040 ... (remaining 18115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 24 through 57) selection = chain 'G' } 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: 0.980 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.007 0.094 2212 Z= 0.323 Angle : 1.152 14.883 3004 Z= 0.572 Chirality : 0.060 0.330 371 Planarity : 0.006 0.038 350 Dihedral : 15.183 75.822 835 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.59 (0.45), residues: 260 helix: -0.99 (0.29), residues: 221 sheet: None (None), residues: 0 loop : -0.09 (1.09), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.006 0.004 HIS A 226 PHE 0.026 0.002 PHE A 207 TYR 0.029 0.004 TYR G 43 ARG 0.011 0.001 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.13330 ( 182) hydrogen bonds : angle 6.69928 ( 543) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.95011 ( 4) covalent geometry : bond 0.00698 ( 2210) covalent geometry : angle 1.15069 ( 3000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.247 Fit side-chains REVERT: C 32 LEU cc_start: 0.8111 (tt) cc_final: 0.7906 (tt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.6876 time to fit residues: 19.4262 Evaluate side-chains 25 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134323 restraints weight = 2590.123| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.57 r_work: 0.3277 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2212 Z= 0.174 Angle : 0.604 5.676 3004 Z= 0.310 Chirality : 0.039 0.119 371 Planarity : 0.004 0.021 350 Dihedral : 10.870 58.752 358 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.27 % Allowed : 8.05 % Favored : 90.68 % 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: 0.38 (0.50), residues: 260 helix: 0.44 (0.32), residues: 226 sheet: None (None), residues: 0 loop : -0.21 (1.16), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.010 0.001 PHE B 102 TYR 0.024 0.002 TYR C 35 ARG 0.003 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 182) hydrogen bonds : angle 4.36064 ( 543) SS BOND : bond 0.00137 ( 2) SS BOND : angle 1.09547 ( 4) covalent geometry : bond 0.00388 ( 2210) covalent geometry : angle 0.60350 ( 3000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.254 Fit side-chains REVERT: A 201 ARG cc_start: 0.8322 (mmt90) cc_final: 0.7999 (tpt-90) REVERT: A 226 HIS cc_start: 0.7087 (t70) cc_final: 0.6711 (t-170) REVERT: A 227 LYS cc_start: 0.7685 (ptmt) cc_final: 0.7405 (ptmm) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.9039 time to fit residues: 28.0890 Evaluate side-chains 30 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.143554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120198 restraints weight = 2651.608| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.64 r_work: 0.3225 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2212 Z= 0.184 Angle : 0.595 5.703 3004 Z= 0.306 Chirality : 0.039 0.129 371 Planarity : 0.003 0.018 350 Dihedral : 10.134 57.890 358 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.85 % Allowed : 12.71 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.50), residues: 260 helix: 0.82 (0.33), residues: 230 sheet: None (None), residues: 0 loop : 0.00 (1.23), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.009 0.001 PHE B 102 TYR 0.023 0.002 TYR C 35 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 182) hydrogen bonds : angle 4.23956 ( 543) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.01082 ( 4) covalent geometry : bond 0.00417 ( 2210) covalent geometry : angle 0.59473 ( 3000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.236 Fit side-chains REVERT: A 201 ARG cc_start: 0.8508 (mmt90) cc_final: 0.8178 (tpt-90) REVERT: A 226 HIS cc_start: 0.7160 (t70) cc_final: 0.6766 (t-170) REVERT: A 227 LYS cc_start: 0.7767 (ptmt) cc_final: 0.7557 (ptmm) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.7798 time to fit residues: 21.9236 Evaluate side-chains 26 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.146292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123318 restraints weight = 2640.139| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.60 r_work: 0.3271 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2212 Z= 0.138 Angle : 0.537 5.524 3004 Z= 0.277 Chirality : 0.036 0.119 371 Planarity : 0.003 0.018 350 Dihedral : 9.285 58.028 358 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.27 % Allowed : 14.41 % Favored : 84.32 % 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: 1.63 (0.50), residues: 260 helix: 1.28 (0.33), residues: 226 sheet: None (None), residues: 0 loop : 0.23 (1.17), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 50 HIS 0.001 0.001 HIS A 226 PHE 0.006 0.001 PHE B 102 TYR 0.018 0.002 TYR C 35 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 182) hydrogen bonds : angle 3.98385 ( 543) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.97205 ( 4) covalent geometry : bond 0.00298 ( 2210) covalent geometry : angle 0.53624 ( 3000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.229 Fit side-chains REVERT: A 201 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8080 (tpt-90) REVERT: A 226 HIS cc_start: 0.7186 (t70) cc_final: 0.6829 (t-170) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.7339 time to fit residues: 22.9348 Evaluate side-chains 29 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 2 optimal weight: 0.0370 chunk 6 optimal weight: 0.5980 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.162915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140345 restraints weight = 2545.969| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.59 r_work: 0.3331 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2212 Z= 0.120 Angle : 0.504 5.562 3004 Z= 0.263 Chirality : 0.035 0.118 371 Planarity : 0.002 0.017 350 Dihedral : 8.884 57.631 358 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.12 % Allowed : 15.25 % Favored : 82.63 % 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: 2.20 (0.51), residues: 260 helix: 1.64 (0.33), residues: 226 sheet: None (None), residues: 0 loop : 0.59 (1.24), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 50 HIS 0.001 0.001 HIS A 226 PHE 0.014 0.001 PHE A 207 TYR 0.017 0.001 TYR C 35 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 182) hydrogen bonds : angle 3.75734 ( 543) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.88977 ( 4) covalent geometry : bond 0.00251 ( 2210) covalent geometry : angle 0.50365 ( 3000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.196 Fit side-chains REVERT: A 201 ARG cc_start: 0.8354 (mmt90) cc_final: 0.7978 (tpt-90) REVERT: A 226 HIS cc_start: 0.7181 (t70) cc_final: 0.6864 (t-170) REVERT: C 34 LEU cc_start: 0.7068 (tt) cc_final: 0.6678 (mt) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.7065 time to fit residues: 24.4111 Evaluate side-chains 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.159856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137933 restraints weight = 2571.830| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.55 r_work: 0.3308 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2212 Z= 0.135 Angle : 0.520 5.670 3004 Z= 0.272 Chirality : 0.036 0.128 371 Planarity : 0.003 0.017 350 Dihedral : 8.950 59.223 358 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.81 % Allowed : 15.25 % Favored : 80.93 % 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: 2.37 (0.51), residues: 260 helix: 1.74 (0.33), residues: 226 sheet: None (None), residues: 0 loop : 0.75 (1.26), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 50 HIS 0.001 0.001 HIS A 226 PHE 0.018 0.001 PHE A 207 TYR 0.014 0.001 TYR B 100 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 182) hydrogen bonds : angle 3.77308 ( 543) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.82828 ( 4) covalent geometry : bond 0.00296 ( 2210) covalent geometry : angle 0.51943 ( 3000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.231 Fit side-chains REVERT: A 201 ARG cc_start: 0.8372 (mmt90) cc_final: 0.7982 (tpt-90) REVERT: C 29 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: G 33 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: G 40 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7648 (m) outliers start: 9 outliers final: 2 residues processed: 30 average time/residue: 0.7225 time to fit residues: 22.5807 Evaluate side-chains 28 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 PHE Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.156144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133385 restraints weight = 2601.146| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.60 r_work: 0.3335 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2212 Z= 0.177 Angle : 0.589 6.682 3004 Z= 0.301 Chirality : 0.038 0.124 371 Planarity : 0.003 0.018 350 Dihedral : 8.891 54.857 358 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.97 % Allowed : 18.22 % Favored : 78.81 % 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: 2.13 (0.51), residues: 260 helix: 1.61 (0.33), residues: 223 sheet: None (None), residues: 0 loop : 0.56 (1.15), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.021 0.001 PHE A 207 TYR 0.017 0.002 TYR C 35 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 182) hydrogen bonds : angle 3.95576 ( 543) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.78519 ( 4) covalent geometry : bond 0.00407 ( 2210) covalent geometry : angle 0.58840 ( 3000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.260 Fit side-chains REVERT: A 201 ARG cc_start: 0.8550 (mmt90) cc_final: 0.8170 (tpt-90) REVERT: A 226 HIS cc_start: 0.7201 (t70) cc_final: 0.6819 (t-170) REVERT: C 29 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: G 40 THR cc_start: 0.8143 (m) cc_final: 0.7924 (m) outliers start: 7 outliers final: 3 residues processed: 32 average time/residue: 0.7275 time to fit residues: 24.2874 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.157093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134977 restraints weight = 2667.852| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.57 r_work: 0.3351 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2212 Z= 0.157 Angle : 0.589 10.469 3004 Z= 0.298 Chirality : 0.037 0.135 371 Planarity : 0.003 0.018 350 Dihedral : 8.602 56.192 358 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.12 % Allowed : 18.64 % Favored : 79.24 % 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: 2.27 (0.51), residues: 260 helix: 1.69 (0.33), residues: 226 sheet: None (None), residues: 0 loop : 0.63 (1.21), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.021 0.001 PHE A 207 TYR 0.015 0.002 TYR B 100 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 182) hydrogen bonds : angle 3.94033 ( 543) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.87571 ( 4) covalent geometry : bond 0.00356 ( 2210) covalent geometry : angle 0.58883 ( 3000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.250 Fit side-chains REVERT: A 201 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8130 (tpt-90) REVERT: A 226 HIS cc_start: 0.7176 (t70) cc_final: 0.6797 (t-170) REVERT: G 40 THR cc_start: 0.8027 (m) cc_final: 0.7780 (m) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.7744 time to fit residues: 23.4014 Evaluate side-chains 27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132850 restraints weight = 2634.305| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.60 r_work: 0.3322 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2212 Z= 0.195 Angle : 0.668 13.443 3004 Z= 0.326 Chirality : 0.039 0.138 371 Planarity : 0.003 0.018 350 Dihedral : 8.791 58.225 358 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.69 % Allowed : 21.19 % Favored : 77.12 % 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 (0.51), residues: 260 helix: 1.45 (0.33), residues: 227 sheet: None (None), residues: 0 loop : 0.49 (1.19), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.024 0.001 PHE A 207 TYR 0.016 0.002 TYR B 100 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 182) hydrogen bonds : angle 4.04141 ( 543) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.82341 ( 4) covalent geometry : bond 0.00454 ( 2210) covalent geometry : angle 0.66769 ( 3000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.256 Fit side-chains REVERT: A 226 HIS cc_start: 0.7203 (t70) cc_final: 0.6799 (t-170) REVERT: B 159 MET cc_start: 0.8651 (mmm) cc_final: 0.8306 (mmm) REVERT: G 40 THR cc_start: 0.8143 (m) cc_final: 0.7924 (m) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.6190 time to fit residues: 18.8812 Evaluate side-chains 30 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.156619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134330 restraints weight = 2585.433| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.57 r_work: 0.3248 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2212 Z= 0.166 Angle : 0.625 13.007 3004 Z= 0.311 Chirality : 0.038 0.129 371 Planarity : 0.003 0.018 350 Dihedral : 8.620 59.040 358 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.85 % Allowed : 21.61 % Favored : 77.54 % 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 (0.51), residues: 260 helix: 1.56 (0.33), residues: 227 sheet: None (None), residues: 0 loop : 0.65 (1.23), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.020 0.001 PHE A 207 TYR 0.016 0.002 TYR B 100 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 182) hydrogen bonds : angle 3.98309 ( 543) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.86994 ( 4) covalent geometry : bond 0.00380 ( 2210) covalent geometry : angle 0.62433 ( 3000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.252 Fit side-chains REVERT: A 226 HIS cc_start: 0.7125 (t70) cc_final: 0.6726 (t-170) REVERT: B 159 MET cc_start: 0.8617 (mmm) cc_final: 0.8104 (mmm) REVERT: G 40 THR cc_start: 0.7991 (m) cc_final: 0.7737 (m) outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.6353 time to fit residues: 18.0735 Evaluate side-chains 27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.156154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133829 restraints weight = 2601.221| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.58 r_work: 0.3244 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2212 Z= 0.184 Angle : 0.653 12.652 3004 Z= 0.323 Chirality : 0.038 0.139 371 Planarity : 0.003 0.018 350 Dihedral : 8.759 59.692 358 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.85 % Allowed : 21.61 % Favored : 77.54 % 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: 2.08 (0.51), residues: 260 helix: 1.54 (0.33), residues: 227 sheet: None (None), residues: 0 loop : 0.65 (1.23), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 50 HIS 0.002 0.001 HIS A 226 PHE 0.023 0.002 PHE A 207 TYR 0.015 0.002 TYR B 100 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 182) hydrogen bonds : angle 4.01598 ( 543) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.85535 ( 4) covalent geometry : bond 0.00427 ( 2210) covalent geometry : angle 0.65270 ( 3000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.60 seconds wall clock time: 31 minutes 11.07 seconds (1871.07 seconds total)