Starting phenix.real_space_refine on Wed Jun 4 13:48:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qct_18335/06_2025/8qct_18335_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qct_18335/06_2025/8qct_18335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qct_18335/06_2025/8qct_18335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qct_18335/06_2025/8qct_18335.map" model { file = "/net/cci-nas-00/data/ceres_data/8qct_18335/06_2025/8qct_18335_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qct_18335/06_2025/8qct_18335_neut.cif" } resolution = 2.6 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= 0.000 sd= 0.005 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 18 5.16 5 C 2167 2.51 5 N 505 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3259 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3252 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.81 Number of scatterers: 3259 At special positions: 0 Unit cell: (81.366, 56.154, 65.322, 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 18 16.00 O 569 8.00 N 505 7.00 C 2167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 405.8 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.093A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 171 removed outlier: 3.712A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.022A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.647A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 removed outlier: 3.803A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.190A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.614A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.124A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 388 Processing helix chain 'A' and resid 397 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.615A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.564A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.556A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.614A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 756 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: 0.95 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 967 1.34 - 1.46: 779 1.46 - 1.58: 1566 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3340 Sorted by residual: bond pdb=" N GLU A 233 " pdb=" CA GLU A 233 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.33e-02 5.65e+03 5.56e+00 bond pdb=" CG ASN A 265 " pdb=" ND2 ASN A 265 " ideal model delta sigma weight residual 1.328 1.351 -0.023 2.10e-02 2.27e+03 1.20e+00 bond pdb=" C LEU A 220 " pdb=" N PRO A 221 " ideal model delta sigma weight residual 1.334 1.348 -0.013 1.51e-02 4.39e+03 7.94e-01 bond pdb=" C TYR A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.80e-01 bond pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.21e-01 ... (remaining 3335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 4393 1.11 - 2.21: 121 2.21 - 3.32: 29 3.32 - 4.43: 7 4.43 - 5.54: 6 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " pdb=" CD GLU A 298 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.70e+00 3.46e-01 5.55e+00 angle pdb=" CA TYR A 117 " pdb=" CB TYR A 117 " pdb=" CG TYR A 117 " ideal model delta sigma weight residual 113.90 117.89 -3.99 1.80e+00 3.09e-01 4.91e+00 angle pdb=" N PRO A 256 " pdb=" CA PRO A 256 " pdb=" C PRO A 256 " ideal model delta sigma weight residual 110.70 113.40 -2.70 1.22e+00 6.72e-01 4.91e+00 angle pdb=" CA PRO A 256 " pdb=" C PRO A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 117.93 120.23 -2.30 1.20e+00 6.94e-01 3.66e+00 angle pdb=" CA GLY A 219 " pdb=" C GLY A 219 " pdb=" N LEU A 220 " ideal model delta sigma weight residual 118.41 116.05 2.36 1.29e+00 6.01e-01 3.34e+00 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 1691 17.44 - 34.89: 171 34.89 - 52.33: 48 52.33 - 69.77: 11 69.77 - 87.22: 3 Dihedral angle restraints: 1924 sinusoidal: 721 harmonic: 1203 Sorted by residual: dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 164.09 15.91 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA GLU A 459 " pdb=" CB GLU A 459 " pdb=" CG GLU A 459 " pdb=" CD GLU A 459 " ideal model delta sinusoidal sigma weight residual -180.00 -120.35 -59.65 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 173 " pdb=" CA LEU A 173 " pdb=" CB LEU A 173 " pdb=" CG LEU A 173 " ideal model delta sinusoidal sigma weight residual -60.00 -117.25 57.25 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 360 0.029 - 0.059: 126 0.059 - 0.088: 40 0.088 - 0.118: 17 0.118 - 0.147: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA GLU A 233 " pdb=" N GLU A 233 " pdb=" C GLU A 233 " pdb=" CB GLU A 233 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA LEU A 220 " pdb=" N LEU A 220 " pdb=" C LEU A 220 " pdb=" CB LEU A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 541 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 104 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 105 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 162 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO A 163 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 303 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.39e+00 pdb=" N PRO A 304 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.016 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 288 2.74 - 3.28: 3401 3.28 - 3.82: 5718 3.82 - 4.36: 6918 4.36 - 4.90: 11519 Nonbonded interactions: 27844 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" OG1 THR A 419 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 350 " pdb=" OE1 GLN A 481 " model vdw 2.223 3.040 nonbonded pdb=" OD2 ASP A 169 " pdb=" OH TYR A 321 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OG1 THR A 203 " model vdw 2.273 3.040 nonbonded pdb=" O THR A 263 " pdb=" OG1 THR A 263 " model vdw 2.326 3.040 ... (remaining 27839 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.300 Find NCS groups from input model: 0.030 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3340 Z= 0.120 Angle : 0.494 5.535 4556 Z= 0.268 Chirality : 0.036 0.147 544 Planarity : 0.004 0.052 552 Dihedral : 15.836 87.215 1158 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 21.75 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.40), residues: 416 helix: 1.04 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.24 (0.61), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 148 HIS 0.003 0.001 HIS A 145 PHE 0.010 0.001 PHE A 114 TYR 0.018 0.001 TYR A 117 ARG 0.007 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.20073 ( 252) hydrogen bonds : angle 7.25046 ( 756) covalent geometry : bond 0.00275 ( 3340) covalent geometry : angle 0.49444 ( 4556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.355 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.2774 time to fit residues: 53.9985 Evaluate side-chains 39 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.0000 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106225 restraints weight = 3756.344| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.51 r_work: 0.3009 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3340 Z= 0.129 Angle : 0.519 5.676 4556 Z= 0.277 Chirality : 0.037 0.154 544 Planarity : 0.005 0.049 552 Dihedral : 4.270 27.569 450 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.26 % Allowed : 18.64 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.43), residues: 416 helix: 2.10 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -2.29 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.001 HIS A 198 PHE 0.012 0.001 PHE A 496 TYR 0.021 0.001 TYR A 117 ARG 0.005 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 252) hydrogen bonds : angle 4.72712 ( 756) covalent geometry : bond 0.00263 ( 3340) covalent geometry : angle 0.51898 ( 4556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7356 (t0) cc_final: 0.7067 (t0) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 1.2072 time to fit residues: 63.5919 Evaluate side-chains 45 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.134666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104503 restraints weight = 3758.976| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.53 r_work: 0.3001 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.129 Angle : 0.511 5.799 4556 Z= 0.272 Chirality : 0.037 0.161 544 Planarity : 0.004 0.044 552 Dihedral : 4.311 29.101 450 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 18.64 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.43), residues: 416 helix: 2.17 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -2.00 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.005 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 252) hydrogen bonds : angle 4.49766 ( 756) covalent geometry : bond 0.00276 ( 3340) covalent geometry : angle 0.51148 ( 4556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8379 (m-30) cc_final: 0.8174 (m-30) REVERT: A 266 ASP cc_start: 0.7247 (t0) cc_final: 0.6759 (t0) REVERT: A 326 ARG cc_start: 0.6700 (ptm160) cc_final: 0.5759 (mtt180) REVERT: A 400 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.6857 (tm-30) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 1.1347 time to fit residues: 57.5061 Evaluate side-chains 44 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.134230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103872 restraints weight = 3883.891| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.55 r_work: 0.3001 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3340 Z= 0.138 Angle : 0.526 5.965 4556 Z= 0.280 Chirality : 0.038 0.167 544 Planarity : 0.004 0.041 552 Dihedral : 4.409 30.210 450 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.95 % Allowed : 18.08 % Favored : 77.97 % 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: 2.19 (0.43), residues: 416 helix: 2.17 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.92 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.003 0.001 HIS A 145 PHE 0.015 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.005 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 252) hydrogen bonds : angle 4.41994 ( 756) covalent geometry : bond 0.00308 ( 3340) covalent geometry : angle 0.52611 ( 4556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8462 (m-30) cc_final: 0.8220 (m-30) REVERT: A 196 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: A 266 ASP cc_start: 0.7342 (t0) cc_final: 0.6771 (t0) REVERT: A 326 ARG cc_start: 0.6740 (ptm160) cc_final: 0.5839 (mtt180) REVERT: A 400 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6863 (tm-30) outliers start: 14 outliers final: 5 residues processed: 52 average time/residue: 1.1028 time to fit residues: 59.2762 Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 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 = 0.3534 r_free = 0.3534 target = 0.135100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.104954 restraints weight = 3833.389| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.54 r_work: 0.2999 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.127 Angle : 0.510 6.023 4556 Z= 0.272 Chirality : 0.037 0.166 544 Planarity : 0.004 0.041 552 Dihedral : 4.388 30.126 450 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.11 % Allowed : 18.36 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.43), residues: 416 helix: 2.22 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.91 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 252) hydrogen bonds : angle 4.32937 ( 756) covalent geometry : bond 0.00277 ( 3340) covalent geometry : angle 0.50999 ( 4556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: A 266 ASP cc_start: 0.7360 (t0) cc_final: 0.6816 (t0) REVERT: A 301 ARG cc_start: 0.7420 (mtp180) cc_final: 0.7197 (ttm110) REVERT: A 326 ARG cc_start: 0.6604 (ptm160) cc_final: 0.5866 (mtt180) REVERT: A 400 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: A 512 LYS cc_start: 0.6769 (mmtt) cc_final: 0.6227 (pptt) outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 1.1111 time to fit residues: 61.9558 Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.135074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105020 restraints weight = 3955.366| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.54 r_work: 0.3000 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3340 Z= 0.137 Angle : 0.525 6.043 4556 Z= 0.280 Chirality : 0.038 0.172 544 Planarity : 0.004 0.040 552 Dihedral : 4.441 30.502 450 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.11 % Allowed : 18.64 % Favored : 78.25 % 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: 2.28 (0.43), residues: 416 helix: 2.30 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.91 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.003 0.001 HIS A 145 PHE 0.016 0.002 PHE A 114 TYR 0.026 0.001 TYR A 117 ARG 0.006 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 252) hydrogen bonds : angle 4.34335 ( 756) covalent geometry : bond 0.00306 ( 3340) covalent geometry : angle 0.52475 ( 4556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.6865 (mp10) REVERT: A 266 ASP cc_start: 0.7413 (t0) cc_final: 0.6813 (t0) REVERT: A 301 ARG cc_start: 0.7445 (mtp180) cc_final: 0.7222 (ttm110) REVERT: A 326 ARG cc_start: 0.6670 (ptm160) cc_final: 0.5938 (mtt180) REVERT: A 400 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: A 512 LYS cc_start: 0.6763 (mmtt) cc_final: 0.6256 (pptt) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 1.1481 time to fit residues: 59.4389 Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106198 restraints weight = 3817.419| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.51 r_work: 0.3049 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.132 Angle : 0.517 6.176 4556 Z= 0.276 Chirality : 0.038 0.170 544 Planarity : 0.004 0.039 552 Dihedral : 4.435 30.659 450 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.82 % Allowed : 18.93 % Favored : 78.25 % 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: 2.31 (0.43), residues: 416 helix: 2.26 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.88 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.015 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.007 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 252) hydrogen bonds : angle 4.31138 ( 756) covalent geometry : bond 0.00292 ( 3340) covalent geometry : angle 0.51677 ( 4556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.6816 (mp10) REVERT: A 266 ASP cc_start: 0.7401 (t0) cc_final: 0.6775 (t0) REVERT: A 301 ARG cc_start: 0.7433 (mtp180) cc_final: 0.7220 (ttm110) REVERT: A 326 ARG cc_start: 0.6680 (ptm160) cc_final: 0.5955 (mtt180) REVERT: A 364 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: A 400 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: A 512 LYS cc_start: 0.6713 (mmtt) cc_final: 0.6277 (pptt) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 1.2103 time to fit residues: 59.9851 Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.106732 restraints weight = 3842.527| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.51 r_work: 0.3000 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.132 Angle : 0.520 6.151 4556 Z= 0.278 Chirality : 0.038 0.170 544 Planarity : 0.004 0.037 552 Dihedral : 4.442 30.650 450 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.54 % Allowed : 18.93 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.43), residues: 416 helix: 2.26 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.89 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.015 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.007 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 252) hydrogen bonds : angle 4.30047 ( 756) covalent geometry : bond 0.00292 ( 3340) covalent geometry : angle 0.52024 ( 4556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: A 201 TRP cc_start: 0.7753 (m100) cc_final: 0.5594 (p-90) REVERT: A 266 ASP cc_start: 0.7378 (t0) cc_final: 0.6767 (t0) REVERT: A 301 ARG cc_start: 0.7467 (mtp180) cc_final: 0.7195 (ttm110) REVERT: A 326 ARG cc_start: 0.6671 (ptm160) cc_final: 0.5949 (mtt180) REVERT: A 400 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: A 512 LYS cc_start: 0.6679 (mmtt) cc_final: 0.6234 (pptt) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.9935 time to fit residues: 48.4349 Evaluate side-chains 50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.0000 chunk 6 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.107237 restraints weight = 3844.446| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.51 r_work: 0.3013 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3340 Z= 0.122 Angle : 0.505 6.131 4556 Z= 0.270 Chirality : 0.037 0.165 544 Planarity : 0.004 0.038 552 Dihedral : 4.373 29.855 450 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.54 % Allowed : 18.64 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.43), residues: 416 helix: 2.33 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.87 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.001 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 252) hydrogen bonds : angle 4.23334 ( 756) covalent geometry : bond 0.00261 ( 3340) covalent geometry : angle 0.50501 ( 4556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: A 201 TRP cc_start: 0.7689 (m100) cc_final: 0.5550 (p-90) REVERT: A 266 ASP cc_start: 0.7260 (t0) cc_final: 0.6683 (t0) REVERT: A 326 ARG cc_start: 0.6691 (ptm160) cc_final: 0.5959 (mtt180) REVERT: A 364 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6970 (pp20) REVERT: A 400 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: A 512 LYS cc_start: 0.6524 (mmtt) cc_final: 0.6144 (pptt) outliers start: 9 outliers final: 2 residues processed: 48 average time/residue: 1.0373 time to fit residues: 51.6480 Evaluate side-chains 45 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107024 restraints weight = 3783.781| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.50 r_work: 0.3017 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3340 Z= 0.124 Angle : 0.510 6.103 4556 Z= 0.273 Chirality : 0.037 0.165 544 Planarity : 0.004 0.039 552 Dihedral : 4.376 29.738 450 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.13 % Allowed : 19.77 % Favored : 79.10 % 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: 2.40 (0.43), residues: 416 helix: 2.33 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.94 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.001 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 252) hydrogen bonds : angle 4.23598 ( 756) covalent geometry : bond 0.00266 ( 3340) covalent geometry : angle 0.51029 ( 4556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: A 201 TRP cc_start: 0.7694 (m100) cc_final: 0.5567 (p-90) REVERT: A 266 ASP cc_start: 0.7305 (t0) cc_final: 0.6641 (t0) REVERT: A 326 ARG cc_start: 0.6628 (ptm160) cc_final: 0.5925 (mtt180) REVERT: A 400 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: A 512 LYS cc_start: 0.6494 (mmtt) cc_final: 0.6227 (pptt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 1.0268 time to fit residues: 46.9212 Evaluate side-chains 46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 400 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107779 restraints weight = 3843.739| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.51 r_work: 0.3022 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3340 Z= 0.121 Angle : 0.506 6.096 4556 Z= 0.270 Chirality : 0.037 0.164 544 Planarity : 0.004 0.038 552 Dihedral : 4.342 28.872 450 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.69 % Allowed : 19.21 % Favored : 79.10 % 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: 2.42 (0.43), residues: 416 helix: 2.36 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -2.00 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.001 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 252) hydrogen bonds : angle 4.20520 ( 756) covalent geometry : bond 0.00259 ( 3340) covalent geometry : angle 0.50558 ( 4556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.67 seconds wall clock time: 46 minutes 49.10 seconds (2809.10 seconds total)