Starting phenix.real_space_refine on Wed Sep 17 03:00:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrc_63325/09_2025/9lrc_63325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrc_63325/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lrc_63325/09_2025/9lrc_63325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrc_63325/09_2025/9lrc_63325_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lrc_63325/09_2025/9lrc_63325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrc_63325/09_2025/9lrc_63325.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.89, per 1000 atoms: 0.38 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: 0.23 Conformation dependent library (CDL) restraints added in 110.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.07 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: 0.36 Time building geometry restraints manager: 0.30 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: 0.930 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.840 Find NCS groups from input model: 0.010 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG R 364 TYR 0.005 0.001 TYR R 198 PHE 0.005 0.001 PHE R 144 TRP 0.007 0.001 TRP R 202 HIS 0.001 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2401) covalent geometry : angle 0.48864 ( 3272) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.67300 ( 2) hydrogen bonds : bond 0.08896 ( 187) hydrogen bonds : angle 4.25550 ( 555) *********************** 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 : 0.080 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: 0.4397 time to fit residues: 16.7559 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 : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.162669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133083 restraints weight = 2563.375| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.62 r_work: 0.3358 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2402 Z= 0.151 Angle : 0.550 7.601 3274 Z= 0.277 Chirality : 0.038 0.132 372 Planarity : 0.005 0.036 389 Dihedral : 6.496 61.925 309 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.79 % Allowed : 9.49 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.49), residues: 278 helix: 2.50 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -0.89 (1.15), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 204 TYR 0.009 0.001 TYR R 358 PHE 0.013 0.001 PHE R 63 TRP 0.008 0.001 TRP R 316 HIS 0.001 0.000 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2401) covalent geometry : angle 0.54928 ( 3272) SS BOND : bond 0.00499 ( 1) SS BOND : angle 1.55859 ( 2) hydrogen bonds : bond 0.05089 ( 187) hydrogen bonds : angle 4.04533 ( 555) *********************** 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 31 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.089 Fit side-chains REVERT: R 61 ASP cc_start: 0.7999 (m-30) cc_final: 0.7795 (m-30) REVERT: R 370 LEU cc_start: 0.8011 (mt) cc_final: 0.7785 (mt) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.4465 time to fit residues: 14.3014 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 : 0.090 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.162862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133227 restraints weight = 2597.603| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.64 r_work: 0.3352 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2402 Z= 0.152 Angle : 0.541 6.357 3274 Z= 0.275 Chirality : 0.038 0.130 372 Planarity : 0.005 0.041 389 Dihedral : 6.093 54.604 309 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.40 % Allowed : 11.07 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.48), residues: 278 helix: 2.31 (0.31), residues: 247 sheet: None (None), residues: 0 loop : -1.33 (1.03), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 204 TYR 0.010 0.001 TYR R 358 PHE 0.012 0.001 PHE R 63 TRP 0.008 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2401) covalent geometry : angle 0.53928 ( 3272) SS BOND : bond 0.00520 ( 1) SS BOND : angle 1.57056 ( 2) hydrogen bonds : bond 0.05152 ( 187) hydrogen bonds : angle 4.04584 ( 555) *********************** 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 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.056 Fit side-chains REVERT: R 125 GLN cc_start: 0.6809 (tp-100) cc_final: 0.5999 (pt0) REVERT: R 155 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8056 (tp30) REVERT: R 370 LEU cc_start: 0.7973 (mt) cc_final: 0.7724 (mt) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.4202 time to fit residues: 12.5708 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 : 0.086 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.0070 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.161756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131811 restraints weight = 2611.032| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.65 r_work: 0.3384 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1569 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 : 0.517 5.601 3274 Z= 0.265 Chirality : 0.037 0.129 372 Planarity : 0.005 0.040 389 Dihedral : 5.687 48.274 309 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.48), residues: 278 helix: 2.35 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.28 (0.98), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 364 TYR 0.010 0.001 TYR R 358 PHE 0.011 0.001 PHE R 63 TRP 0.008 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2401) covalent geometry : angle 0.51546 ( 3272) SS BOND : bond 0.00468 ( 1) SS BOND : angle 1.49465 ( 2) hydrogen bonds : bond 0.04943 ( 187) hydrogen bonds : angle 4.01140 ( 555) *********************** 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 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.099 Fit side-chains REVERT: R 125 GLN cc_start: 0.6774 (tp-100) cc_final: 0.5996 (pt0) REVERT: R 155 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8030 (tp30) REVERT: R 370 LEU cc_start: 0.7984 (mt) cc_final: 0.7721 (mt) outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.4093 time to fit residues: 13.5547 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 : 0.088 ------------------------------------------------------------------------------- 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 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 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 = 0.3777 r_free = 0.3777 target = 0.159957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130109 restraints weight = 2566.167| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.63 r_work: 0.3344 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1684 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= 0.162 Angle : 0.545 7.072 3274 Z= 0.277 Chirality : 0.038 0.136 372 Planarity : 0.005 0.047 389 Dihedral : 5.894 49.359 309 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.48), residues: 278 helix: 2.26 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.46 (0.91), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 204 TYR 0.012 0.001 TYR R 358 PHE 0.014 0.001 PHE R 63 TRP 0.008 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 2401) covalent geometry : angle 0.54336 ( 3272) SS BOND : bond 0.00552 ( 1) SS BOND : angle 1.61939 ( 2) hydrogen bonds : bond 0.05310 ( 187) hydrogen bonds : angle 4.06926 ( 555) *********************** 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 : 0.087 Fit side-chains REVERT: R 125 GLN cc_start: 0.6752 (tp-100) cc_final: 0.6010 (pt0) REVERT: R 370 LEU cc_start: 0.8013 (mt) cc_final: 0.7748 (mt) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.3971 time to fit residues: 13.1554 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 : 0.089 ------------------------------------------------------------------------------- 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 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 27 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 = 0.3787 r_free = 0.3787 target = 0.160849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131065 restraints weight = 2541.588| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.61 r_work: 0.3339 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1791 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 : 0.540 6.113 3274 Z= 0.278 Chirality : 0.039 0.132 372 Planarity : 0.005 0.046 389 Dihedral : 5.772 46.836 309 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.48), residues: 278 helix: 2.18 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.40 (0.92), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 204 TYR 0.011 0.001 TYR R 358 PHE 0.014 0.001 PHE R 63 TRP 0.008 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2401) covalent geometry : angle 0.53825 ( 3272) SS BOND : bond 0.00618 ( 1) SS BOND : angle 1.85695 ( 2) hydrogen bonds : bond 0.05275 ( 187) hydrogen bonds : angle 4.07004 ( 555) *********************** 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 : 0.056 Fit side-chains REVERT: R 125 GLN cc_start: 0.6724 (tp-100) cc_final: 0.6017 (pt0) REVERT: R 370 LEU cc_start: 0.7987 (mt) cc_final: 0.7714 (mt) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.4493 time to fit residues: 14.8561 Evaluate side-chains 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.162412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132693 restraints weight = 2570.421| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.63 r_work: 0.3357 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2402 Z= 0.138 Angle : 0.518 6.146 3274 Z= 0.266 Chirality : 0.038 0.127 372 Planarity : 0.005 0.047 389 Dihedral : 5.286 39.678 309 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.79 % Allowed : 13.44 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.48), residues: 278 helix: 2.25 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.36 (0.95), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 112 TYR 0.009 0.001 TYR R 358 PHE 0.011 0.001 PHE R 63 TRP 0.008 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2401) covalent geometry : angle 0.51695 ( 3272) SS BOND : bond 0.00493 ( 1) SS BOND : angle 1.70017 ( 2) hydrogen bonds : bond 0.04841 ( 187) hydrogen bonds : angle 3.99019 ( 555) *********************** 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: 2 poor density : 31 time to evaluate : 0.095 Fit side-chains REVERT: R 112 ARG cc_start: 0.8314 (mtm180) cc_final: 0.7730 (mtt180) REVERT: R 125 GLN cc_start: 0.6762 (tp-100) cc_final: 0.6025 (pt0) REVERT: R 370 LEU cc_start: 0.8033 (mt) cc_final: 0.7764 (mt) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.4911 time to fit residues: 16.6607 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 : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 316 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3950 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.162533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132926 restraints weight = 2542.123| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.61 r_work: 0.3371 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1977 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= 0.134 Angle : 0.542 7.999 3274 Z= 0.271 Chirality : 0.038 0.126 372 Planarity : 0.005 0.048 389 Dihedral : 5.034 36.045 309 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.58 % Allowed : 13.83 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.48), residues: 278 helix: 2.30 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.26 (0.96), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 364 TYR 0.008 0.001 TYR R 358 PHE 0.011 0.001 PHE R 63 TRP 0.007 0.001 TRP R 316 HIS 0.001 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2401) covalent geometry : angle 0.54089 ( 3272) SS BOND : bond 0.00505 ( 1) SS BOND : angle 1.71993 ( 2) hydrogen bonds : bond 0.04727 ( 187) hydrogen bonds : angle 3.99110 ( 555) *********************** 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 34 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.088 Fit side-chains REVERT: R 112 ARG cc_start: 0.8304 (mtm180) cc_final: 0.7722 (mtt180) REVERT: R 125 GLN cc_start: 0.6753 (tp-100) cc_final: 0.6022 (pt0) REVERT: R 370 LEU cc_start: 0.8023 (mt) cc_final: 0.7755 (mt) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.4462 time to fit residues: 15.6361 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 : 0.092 ------------------------------------------------------------------------------- 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 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 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 = 0.3786 r_free = 0.3786 target = 0.160682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130841 restraints weight = 2589.187| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.63 r_work: 0.3326 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2004 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= 0.169 Angle : 0.593 10.173 3274 Z= 0.294 Chirality : 0.039 0.136 372 Planarity : 0.005 0.053 389 Dihedral : 5.424 39.411 309 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.58 % Allowed : 13.83 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.48), residues: 278 helix: 2.14 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.36 (0.91), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 204 TYR 0.011 0.001 TYR R 358 PHE 0.015 0.001 PHE R 63 TRP 0.007 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2401) covalent geometry : angle 0.59129 ( 3272) SS BOND : bond 0.00624 ( 1) SS BOND : angle 1.97081 ( 2) hydrogen bonds : bond 0.05327 ( 187) hydrogen bonds : angle 4.08554 ( 555) *********************** 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 33 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.088 Fit side-chains REVERT: R 125 GLN cc_start: 0.6731 (tp-100) cc_final: 0.6032 (pt0) REVERT: R 370 LEU cc_start: 0.8053 (mt) cc_final: 0.7775 (mt) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.3504 time to fit residues: 11.9758 Evaluate side-chains 33 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 156 SER 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 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132509 restraints weight = 2591.844| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.63 r_work: 0.3351 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2028 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= 0.161 Angle : 0.585 9.894 3274 Z= 0.291 Chirality : 0.039 0.133 372 Planarity : 0.005 0.054 389 Dihedral : 5.285 35.862 309 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.58 % Allowed : 14.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.48), residues: 278 helix: 2.15 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.36 (0.91), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 204 TYR 0.010 0.001 TYR R 358 PHE 0.014 0.001 PHE R 63 TRP 0.007 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 2401) covalent geometry : angle 0.58323 ( 3272) SS BOND : bond 0.00596 ( 1) SS BOND : angle 1.95130 ( 2) hydrogen bonds : bond 0.05172 ( 187) hydrogen bonds : angle 4.09082 ( 555) ********************** 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: 4 poor density : 30 time to evaluate : 0.086 Fit side-chains REVERT: R 112 ARG cc_start: 0.8387 (mtm180) cc_final: 0.7806 (mtt180) REVERT: R 125 GLN cc_start: 0.6755 (tp-100) cc_final: 0.6042 (pt0) REVERT: R 370 LEU cc_start: 0.8042 (mt) cc_final: 0.7766 (mt) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.3684 time to fit residues: 12.5871 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 : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 156 SER 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 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.159889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129877 restraints weight = 2633.397| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.64 r_work: 0.3360 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2084 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 : 0.609 9.626 3274 Z= 0.305 Chirality : 0.040 0.143 372 Planarity : 0.005 0.056 389 Dihedral : 5.527 38.706 309 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.48), residues: 278 helix: 2.06 (0.31), residues: 246 sheet: None (None), residues: 0 loop : -1.42 (0.89), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 204 TYR 0.012 0.001 TYR R 358 PHE 0.017 0.001 PHE R 63 TRP 0.007 0.001 TRP R 316 HIS 0.002 0.000 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 2401) covalent geometry : angle 0.60700 ( 3272) SS BOND : bond 0.00665 ( 1) SS BOND : angle 2.09416 ( 2) hydrogen bonds : bond 0.05528 ( 187) hydrogen bonds : angle 4.15924 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 992.82 seconds wall clock time: 17 minutes 35.18 seconds (1055.18 seconds total)