Starting phenix.real_space_refine on Wed Jul 23 08:12:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrc_63325/07_2025/9lrc_63325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrc_63325/07_2025/9lrc_63325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lrc_63325/07_2025/9lrc_63325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrc_63325/07_2025/9lrc_63325.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrc_63325/07_2025/9lrc_63325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrc_63325/07_2025/9lrc_63325_neut.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.081 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 11 5.16 5 C 1569 2.51 5 N 366 2.21 5 O 382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2328 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2319 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.35, per 1000 atoms: 1.01 Number of scatterers: 2328 At special positions: 0 Unit cell: (69.72, 71.6566, 69.72, 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 11 16.00 O 382 8.00 N 366 7.00 C 1569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " 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: 0.61 Conformation dependent library (CDL) restraints added in 251.2 milliseconds 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 90.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 11 through 44 removed outlier: 3.576A pdb=" N ASN R 33 " --> pdb=" O ILE R 29 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS R 44 " --> pdb=" O PHE R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 Processing helix chain 'R' and resid 67 through 77 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 Processing helix chain 'R' and resid 118 through 125 Processing helix chain 'R' and resid 128 through 155 removed outlier: 3.856A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix removed outlier: 3.635A pdb=" N VAL R 153 " --> pdb=" O PRO R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 171 through 183 removed outlier: 3.627A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 205 Processing helix chain 'R' and resid 290 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.968A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 362 through 374 187 hydrogen bonds defined for protein. 555 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: 0.64 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: 1.23 - 1.35: 672 1.35 - 1.47: 707 1.47 - 1.59: 1006 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 2401 Sorted by residual: bond pdb=" CA HSM R 701 " pdb=" CB HSM R 701 " ideal model delta sigma weight residual 1.533 1.512 0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" N HSM R 701 " pdb=" CA HSM R 701 " ideal model delta sigma weight residual 1.467 1.485 -0.018 2.00e-02 2.50e+03 8.00e-01 bond pdb=" CE1 HSM R 701 " pdb=" NE2 HSM R 701 " ideal model delta sigma weight residual 1.354 1.338 0.016 2.00e-02 2.50e+03 6.11e-01 bond pdb=" CB PRO R 359 " pdb=" CG PRO R 359 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.90e-01 bond pdb=" CA ILE R 73 " pdb=" CB ILE R 73 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 4.38e-01 ... (remaining 2396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 3133 0.97 - 1.94: 100 1.94 - 2.91: 27 2.91 - 3.88: 7 3.88 - 4.85: 5 Bond angle restraints: 3272 Sorted by residual: angle pdb=" C VAL R 66 " pdb=" CA VAL R 66 " pdb=" CB VAL R 66 " ideal model delta sigma weight residual 112.16 107.99 4.17 1.63e+00 3.76e-01 6.54e+00 angle pdb=" C ILE R 69 " pdb=" CA ILE R 69 " pdb=" CB ILE R 69 " ideal model delta sigma weight residual 114.00 111.23 2.77 1.31e+00 5.83e-01 4.47e+00 angle pdb=" N ILE R 69 " pdb=" CA ILE R 69 " pdb=" C ILE R 69 " ideal model delta sigma weight residual 112.35 110.06 2.29 1.20e+00 6.94e-01 3.63e+00 angle pdb=" C VAL R 66 " pdb=" N ILE R 67 " pdb=" CA ILE R 67 " ideal model delta sigma weight residual 123.08 121.16 1.92 1.01e+00 9.80e-01 3.61e+00 angle pdb=" N VAL R 66 " pdb=" CA VAL R 66 " pdb=" C VAL R 66 " ideal model delta sigma weight residual 111.44 113.97 -2.53 1.34e+00 5.57e-01 3.56e+00 ... (remaining 3267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.96: 1176 13.96 - 27.91: 143 27.91 - 41.87: 32 41.87 - 55.82: 6 55.82 - 69.78: 8 Dihedral angle restraints: 1365 sinusoidal: 525 harmonic: 840 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual 93.00 129.55 -36.55 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA PHE R 63 " pdb=" C PHE R 63 " pdb=" N VAL R 64 " pdb=" CA VAL R 64 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLU R 294 " pdb=" CB GLU R 294 " pdb=" CG GLU R 294 " pdb=" CD GLU R 294 " ideal model delta sinusoidal sigma weight residual -60.00 -119.40 59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 208 0.019 - 0.037: 84 0.037 - 0.056: 27 0.056 - 0.075: 33 0.075 - 0.093: 20 Chirality restraints: 372 Sorted by residual: chirality pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" C PRO R 355 " pdb=" CB PRO R 355 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.18e-01 chirality pdb=" CA ILE R 151 " pdb=" N ILE R 151 " pdb=" C ILE R 151 " pdb=" CB ILE R 151 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.17e-01 chirality pdb=" CA ILE R 197 " pdb=" N ILE R 197 " pdb=" C ILE R 197 " pdb=" CB ILE R 197 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.13e-01 ... (remaining 369 not shown) Planarity restraints: 389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 358 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO R 359 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 359 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 359 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 185 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO R 186 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 186 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 186 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.29e-01 pdb=" N PRO R 149 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.013 5.00e-02 4.00e+02 ... (remaining 386 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1105 2.95 - 3.44: 2557 3.44 - 3.93: 3941 3.93 - 4.41: 4559 4.41 - 4.90: 7249 Nonbonded interactions: 19411 Sorted by model distance: nonbonded pdb=" O LEU R 57 " pdb=" OG SER R 60 " model vdw 2.464 3.040 nonbonded pdb=" O VAL R 88 " pdb=" OG1 THR R 92 " model vdw 2.494 3.040 nonbonded pdb=" O LEU R 326 " pdb=" N SER R 331 " model vdw 2.502 3.120 nonbonded pdb=" O PHE R 344 " pdb=" NE2 HSM R 701 " model vdw 2.545 3.120 nonbonded pdb=" O MET R 150 " pdb=" OG SER R 154 " model vdw 2.576 3.040 ... (remaining 19406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2402 Z= 0.125 Angle : 0.490 4.851 3274 Z= 0.290 Chirality : 0.034 0.093 372 Planarity : 0.004 0.041 389 Dihedral : 13.880 69.778 816 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.50), residues: 278 helix: 2.63 (0.32), residues: 247 sheet: None (None), residues: 0 loop : -1.13 (1.04), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 202 HIS 0.001 0.001 HIS R 126 PHE 0.005 0.001 PHE R 144 TYR 0.005 0.001 TYR R 198 ARG 0.003 0.000 ARG R 364 Details of bonding type rmsd hydrogen bonds : bond 0.08896 ( 187) hydrogen bonds : angle 4.25550 ( 555) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.67300 ( 2) covalent geometry : bond 0.00234 ( 2401) covalent geometry : angle 0.48864 ( 3272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.240 Fit side-chains REVERT: R 112 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7778 (mtt180) REVERT: R 363 LYS cc_start: 0.7787 (mmtt) cc_final: 0.6955 (mppt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.8579 time to fit residues: 32.8516 Evaluate side-chains 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.163825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134225 restraints weight = 2569.020| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.63 r_work: 0.3357 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2402 Z= 0.152 Angle : 0.558 8.172 3274 Z= 0.280 Chirality : 0.038 0.132 372 Planarity : 0.005 0.036 389 Dihedral : 6.504 61.749 309 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.79 % Allowed : 9.88 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.49), residues: 278 helix: 2.48 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -0.88 (1.16), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.001 0.000 HIS R 75 PHE 0.013 0.001 PHE R 63 TYR 0.009 0.001 TYR R 358 ARG 0.002 0.001 ARG R 364 Details of bonding type rmsd hydrogen bonds : bond 0.05130 ( 187) hydrogen bonds : angle 4.05828 ( 555) SS BOND : bond 0.00505 ( 1) SS BOND : angle 1.56394 ( 2) covalent geometry : bond 0.00342 ( 2401) covalent geometry : angle 0.55733 ( 3272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.244 Fit side-chains REVERT: R 61 ASP cc_start: 0.8001 (m-30) cc_final: 0.7795 (m-30) REVERT: R 370 LEU cc_start: 0.8006 (mt) cc_final: 0.7778 (mt) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.8620 time to fit residues: 26.8622 Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.160286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130476 restraints weight = 2518.746| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.61 r_work: 0.3324 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2402 Z= 0.172 Angle : 0.558 6.562 3274 Z= 0.285 Chirality : 0.039 0.136 372 Planarity : 0.005 0.045 389 Dihedral : 6.304 55.844 309 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.40 % Allowed : 10.67 % Favored : 88.93 % 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: 2.76 (0.48), residues: 278 helix: 2.21 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.35 (0.98), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 PHE 0.014 0.001 PHE R 63 TYR 0.012 0.001 TYR R 358 ARG 0.002 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05513 ( 187) hydrogen bonds : angle 4.10081 ( 555) SS BOND : bond 0.00590 ( 1) SS BOND : angle 1.70584 ( 2) covalent geometry : bond 0.00401 ( 2401) covalent geometry : angle 0.55661 ( 3272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.252 Fit side-chains REVERT: R 125 GLN cc_start: 0.6816 (tp-100) cc_final: 0.6023 (pt0) REVERT: R 155 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8081 (tp30) REVERT: R 370 LEU cc_start: 0.8000 (mt) cc_final: 0.7774 (mt) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.9007 time to fit residues: 27.9883 Evaluate side-chains 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.160136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130166 restraints weight = 2530.651| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.62 r_work: 0.3372 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2402 Z= 0.142 Angle : 0.518 5.560 3274 Z= 0.266 Chirality : 0.037 0.129 372 Planarity : 0.005 0.041 389 Dihedral : 5.744 48.180 309 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.19 % Allowed : 11.07 % Favored : 87.75 % 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: 2.89 (0.48), residues: 278 helix: 2.31 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.41 (0.98), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 PHE 0.012 0.001 PHE R 63 TYR 0.009 0.001 TYR R 358 ARG 0.001 0.000 ARG R 364 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 187) hydrogen bonds : angle 4.03548 ( 555) SS BOND : bond 0.00476 ( 1) SS BOND : angle 1.51050 ( 2) covalent geometry : bond 0.00318 ( 2401) covalent geometry : angle 0.51728 ( 3272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.221 Fit side-chains REVERT: R 125 GLN cc_start: 0.6760 (tp-100) cc_final: 0.5984 (pt0) REVERT: R 155 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7987 (tp30) REVERT: R 370 LEU cc_start: 0.7972 (mt) cc_final: 0.7702 (mt) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.7642 time to fit residues: 26.2790 Evaluate side-chains 31 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.163356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133670 restraints weight = 2602.161| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.64 r_work: 0.3398 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2402 Z= 0.133 Angle : 0.514 6.896 3274 Z= 0.260 Chirality : 0.037 0.127 372 Planarity : 0.005 0.042 389 Dihedral : 5.379 42.662 309 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.19 % Allowed : 12.25 % Favored : 86.56 % 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: 2.99 (0.48), residues: 278 helix: 2.37 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.33 (0.96), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 PHE 0.011 0.001 PHE R 63 TYR 0.009 0.001 TYR R 358 ARG 0.001 0.000 ARG R 364 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 187) hydrogen bonds : angle 3.98451 ( 555) SS BOND : bond 0.00443 ( 1) SS BOND : angle 1.41075 ( 2) covalent geometry : bond 0.00292 ( 2401) covalent geometry : angle 0.51305 ( 3272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.230 Fit side-chains REVERT: R 61 ASP cc_start: 0.7883 (m-30) cc_final: 0.7625 (m-30) REVERT: R 125 GLN cc_start: 0.6755 (tp-100) cc_final: 0.6000 (pt0) REVERT: R 155 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7978 (tp30) REVERT: R 370 LEU cc_start: 0.8031 (mt) cc_final: 0.7762 (mt) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.7918 time to fit residues: 26.3731 Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.160186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130332 restraints weight = 2540.091| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.61 r_work: 0.3323 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2402 Z= 0.182 Angle : 0.553 6.444 3274 Z= 0.284 Chirality : 0.039 0.139 372 Planarity : 0.005 0.048 389 Dihedral : 5.904 48.152 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.19 % Allowed : 11.86 % Favored : 86.96 % 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: 2.72 (0.48), residues: 278 helix: 2.20 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.48 (0.90), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 PHE 0.016 0.001 PHE R 63 TYR 0.012 0.001 TYR R 358 ARG 0.002 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 187) hydrogen bonds : angle 4.12075 ( 555) SS BOND : bond 0.00611 ( 1) SS BOND : angle 1.78337 ( 2) covalent geometry : bond 0.00428 ( 2401) covalent geometry : angle 0.55118 ( 3272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.258 Fit side-chains REVERT: R 125 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6010 (pt0) REVERT: R 370 LEU cc_start: 0.7996 (mt) cc_final: 0.7718 (mt) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.7969 time to fit residues: 26.5106 Evaluate side-chains 31 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 24 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 = 0.3779 r_free = 0.3779 target = 0.160104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130118 restraints weight = 2619.795| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.64 r_work: 0.3327 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2402 Z= 0.162 Angle : 0.544 6.456 3274 Z= 0.280 Chirality : 0.039 0.137 372 Planarity : 0.005 0.051 389 Dihedral : 5.672 43.783 309 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.19 % Allowed : 13.44 % Favored : 85.38 % 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: 2.63 (0.48), residues: 278 helix: 2.14 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.49 (0.90), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 PHE 0.014 0.001 PHE R 63 TYR 0.011 0.001 TYR R 358 ARG 0.001 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05271 ( 187) hydrogen bonds : angle 4.06492 ( 555) SS BOND : bond 0.00617 ( 1) SS BOND : angle 1.92392 ( 2) covalent geometry : bond 0.00374 ( 2401) covalent geometry : angle 0.54170 ( 3272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.249 Fit side-chains REVERT: R 125 GLN cc_start: 0.6721 (tp-100) cc_final: 0.6008 (pt0) REVERT: R 370 LEU cc_start: 0.8019 (mt) cc_final: 0.7734 (mt) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.7673 time to fit residues: 26.3647 Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 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 = 0.3776 r_free = 0.3776 target = 0.159769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129672 restraints weight = 2645.209| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.65 r_work: 0.3350 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2402 Z= 0.163 Angle : 0.561 7.631 3274 Z= 0.284 Chirality : 0.039 0.134 372 Planarity : 0.005 0.050 389 Dihedral : 5.597 41.323 309 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.58 % Allowed : 13.44 % Favored : 84.98 % 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: 2.57 (0.48), residues: 278 helix: 2.11 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.56 (0.90), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 PHE 0.014 0.001 PHE R 63 TYR 0.012 0.001 TYR R 358 ARG 0.001 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 187) hydrogen bonds : angle 4.10232 ( 555) SS BOND : bond 0.00610 ( 1) SS BOND : angle 1.94662 ( 2) covalent geometry : bond 0.00378 ( 2401) covalent geometry : angle 0.55880 ( 3272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.199 Fit side-chains REVERT: R 112 ARG cc_start: 0.8403 (mtm180) cc_final: 0.7819 (mtt180) REVERT: R 125 GLN cc_start: 0.6750 (tp-100) cc_final: 0.6034 (pt0) REVERT: R 370 LEU cc_start: 0.8029 (mt) cc_final: 0.7754 (mt) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.8827 time to fit residues: 31.9148 Evaluate side-chains 33 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 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 = 0.3785 r_free = 0.3785 target = 0.160690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130790 restraints weight = 2570.988| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.62 r_work: 0.3326 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2402 Z= 0.157 Angle : 0.583 10.221 3274 Z= 0.289 Chirality : 0.039 0.165 372 Planarity : 0.005 0.052 389 Dihedral : 5.384 37.298 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.19 % Allowed : 14.62 % Favored : 84.19 % 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: 2.58 (0.48), residues: 278 helix: 2.12 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.62 (0.89), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 PHE 0.013 0.001 PHE R 63 TYR 0.010 0.001 TYR R 358 ARG 0.001 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 187) hydrogen bonds : angle 4.08492 ( 555) SS BOND : bond 0.00588 ( 1) SS BOND : angle 2.06066 ( 2) covalent geometry : bond 0.00360 ( 2401) covalent geometry : angle 0.58077 ( 3272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.252 Fit side-chains REVERT: R 112 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7934 (mtt180) REVERT: R 125 GLN cc_start: 0.6764 (tp-100) cc_final: 0.6056 (pt0) REVERT: R 370 LEU cc_start: 0.8039 (mt) cc_final: 0.7761 (mt) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.9049 time to fit residues: 31.8330 Evaluate side-chains 34 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.161294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131314 restraints weight = 2583.118| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.63 r_work: 0.3367 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2402 Z= 0.155 Angle : 0.581 9.891 3274 Z= 0.287 Chirality : 0.039 0.132 372 Planarity : 0.005 0.052 389 Dihedral : 5.238 34.067 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.19 % Allowed : 14.62 % Favored : 84.19 % 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 (0.47), residues: 278 helix: 2.17 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.68 (0.87), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 PHE 0.013 0.001 PHE R 63 TYR 0.011 0.001 TYR R 358 ARG 0.001 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 187) hydrogen bonds : angle 4.10062 ( 555) SS BOND : bond 0.00599 ( 1) SS BOND : angle 2.09616 ( 2) covalent geometry : bond 0.00355 ( 2401) covalent geometry : angle 0.57869 ( 3272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.247 Fit side-chains REVERT: R 112 ARG cc_start: 0.8384 (mtm180) cc_final: 0.7922 (mtt180) REVERT: R 125 GLN cc_start: 0.6742 (tp-100) cc_final: 0.6044 (pt0) REVERT: R 370 LEU cc_start: 0.8038 (mt) cc_final: 0.7765 (mt) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.8419 time to fit residues: 29.6820 Evaluate side-chains 34 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.160535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130665 restraints weight = 2524.590| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.59 r_work: 0.3331 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2402 Z= 0.171 Angle : 0.595 9.562 3274 Z= 0.297 Chirality : 0.040 0.142 372 Planarity : 0.005 0.055 389 Dihedral : 5.350 36.674 309 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.58 % Allowed : 14.62 % Favored : 83.79 % 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: 2.50 (0.47), residues: 278 helix: 2.07 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.68 (0.86), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 PHE 0.015 0.001 PHE R 63 TYR 0.010 0.001 TYR R 358 ARG 0.002 0.000 ARG R 204 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 187) hydrogen bonds : angle 4.14346 ( 555) SS BOND : bond 0.00657 ( 1) SS BOND : angle 2.17895 ( 2) covalent geometry : bond 0.00399 ( 2401) covalent geometry : angle 0.59257 ( 3272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.81 seconds wall clock time: 35 minutes 35.92 seconds (2135.92 seconds total)