Starting phenix.real_space_refine on Wed Sep 17 03:19:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jto_61814/09_2025/9jto_61814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jto_61814/09_2025/9jto_61814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jto_61814/09_2025/9jto_61814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jto_61814/09_2025/9jto_61814.map" model { file = "/net/cci-nas-00/data/ceres_data/9jto_61814/09_2025/9jto_61814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jto_61814/09_2025/9jto_61814.cif" } resolution = 3.3 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= 0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 12 5.16 5 C 1874 2.51 5 N 442 2.21 5 O 487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2817 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'F6P': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P5S:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 0.96, per 1000 atoms: 0.34 Number of scatterers: 2817 At special positions: 0 Unit cell: (68, 83.3, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 2 15.00 O 487 8.00 N 442 7.00 C 1874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 245 " 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: 0.36 Conformation dependent library (CDL) restraints added in 118.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 75.4% 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 'A' and resid 2 through 23 removed outlier: 3.828A pdb=" N LEU A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.876A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.970A pdb=" N ILE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 80 removed outlier: 3.852A pdb=" N GLY A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 138 Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.795A pdb=" N VAL A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 183 " --> pdb=" O HIS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.544A pdb=" N TYR A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.584A pdb=" N LYS A 240 " --> pdb=" O TRP A 236 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.594A pdb=" N ASN A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.741A pdb=" N ARG A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.950A pdb=" N SER A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 175 hydrogen bonds defined for protein. 525 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: 0.37 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 417 1.31 - 1.44: 875 1.44 - 1.57: 1589 1.57 - 1.69: 5 1.69 - 1.82: 17 Bond restraints: 2903 Sorted by residual: bond pdb=" C3 F6P A 702 " pdb=" C4 F6P A 702 " ideal model delta sigma weight residual 1.628 1.248 0.380 2.00e-02 2.50e+03 3.61e+02 bond pdb=" C2 F6P A 702 " pdb=" C3 F6P A 702 " ideal model delta sigma weight residual 1.325 1.640 -0.315 2.00e-02 2.50e+03 2.48e+02 bond pdb=" C2 F6P A 702 " pdb=" O5 F6P A 702 " ideal model delta sigma weight residual 1.600 1.309 0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C4 F6P A 702 " pdb=" C5 F6P A 702 " ideal model delta sigma weight residual 1.367 1.586 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C5 F6P A 702 " pdb=" C6 F6P A 702 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.41e+01 ... (remaining 2898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 3942 4.09 - 8.17: 17 8.17 - 12.26: 1 12.26 - 16.35: 0 16.35 - 20.43: 1 Bond angle restraints: 3961 Sorted by residual: angle pdb=" O13 P5S A 701 " pdb=" P12 P5S A 701 " pdb=" O15 P5S A 701 " ideal model delta sigma weight residual 121.25 100.82 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" CA ASN A 176 " pdb=" C ASN A 176 " pdb=" O ASN A 176 " ideal model delta sigma weight residual 121.40 117.30 4.10 1.13e+00 7.83e-01 1.32e+01 angle pdb=" C20 P5S A 701 " pdb=" C17 P5S A 701 " pdb=" O19 P5S A 701 " ideal model delta sigma weight residual 111.29 120.48 -9.19 3.00e+00 1.11e-01 9.37e+00 angle pdb=" CA ASN A 176 " pdb=" CB ASN A 176 " pdb=" CG ASN A 176 " ideal model delta sigma weight residual 112.60 115.39 -2.79 1.00e+00 1.00e+00 7.79e+00 angle pdb=" OG P5S A 701 " pdb=" P12 P5S A 701 " pdb=" O16 P5S A 701 " ideal model delta sigma weight residual 102.49 110.43 -7.94 3.00e+00 1.11e-01 7.01e+00 ... (remaining 3956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 1635 33.64 - 67.28: 39 67.28 - 100.92: 3 100.92 - 134.56: 2 134.56 - 168.20: 2 Dihedral angle restraints: 1681 sinusoidal: 672 harmonic: 1009 Sorted by residual: dihedral pdb=" C21 P5S A 701 " pdb=" C22 P5S A 701 " pdb=" C23 P5S A 701 " pdb=" C24 P5S A 701 " ideal model delta sinusoidal sigma weight residual -64.63 103.57 -168.20 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CB CYS A 109 " pdb=" SG CYS A 109 " pdb=" SG CYS A 245 " pdb=" CB CYS A 245 " ideal model delta sinusoidal sigma weight residual 93.00 130.43 -37.43 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CB P5S A 701 " pdb=" OG P5S A 701 " pdb=" P12 P5S A 701 " pdb=" O16 P5S A 701 " ideal model delta sinusoidal sigma weight residual 295.68 154.62 141.06 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 1678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 317 0.040 - 0.080: 101 0.080 - 0.119: 24 0.119 - 0.159: 4 0.159 - 0.199: 1 Chirality restraints: 447 Sorted by residual: chirality pdb=" CA P5S A 701 " pdb=" N P5S A 701 " pdb=" C P5S A 701 " pdb=" CB P5S A 701 " both_signs ideal model delta sigma weight residual False 2.40 2.60 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA TYR A 85 " pdb=" N TYR A 85 " pdb=" C TYR A 85 " pdb=" CB TYR A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA PHE A 195 " pdb=" N PHE A 195 " pdb=" C PHE A 195 " pdb=" CB PHE A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 444 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " 0.020 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP A 86 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 115 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 116 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 256 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.31e+00 pdb=" N PRO A 257 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.016 5.00e-02 4.00e+02 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 630 2.79 - 3.31: 2643 3.31 - 3.84: 4453 3.84 - 4.37: 4758 4.37 - 4.90: 8918 Nonbonded interactions: 21402 Sorted by model distance: nonbonded pdb=" OD1 ASP A 92 " pdb=" OG SER A 95 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A 34 " pdb=" NH1 ARG A 170 " model vdw 2.481 3.120 nonbonded pdb=" N P5S A 701 " pdb=" OG P5S A 701 " model vdw 2.481 2.496 nonbonded pdb=" OG1 THR A 111 " pdb=" O THR A 255 " model vdw 2.483 3.040 nonbonded pdb=" O ASP A 92 " pdb=" OD1 ASP A 92 " model vdw 2.483 3.040 ... (remaining 21397 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: 1.070 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.012 0.380 2904 Z= 0.613 Angle : 0.744 20.432 3963 Z= 0.340 Chirality : 0.041 0.199 447 Planarity : 0.004 0.032 476 Dihedral : 16.879 168.204 1028 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 2.01 (0.50), residues: 342 helix: 2.55 (0.36), residues: 244 sheet: None (None), residues: 0 loop : -2.04 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.018 0.001 TYR A 85 PHE 0.013 0.001 PHE A 148 TRP 0.045 0.001 TRP A 86 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.01225 ( 2903) covalent geometry : angle 0.74344 ( 3961) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.07307 ( 2) hydrogen bonds : bond 0.10748 ( 175) hydrogen bonds : angle 4.56506 ( 525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0449 time to fit residues: 2.0706 Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129783 restraints weight = 3449.433| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.87 r_work: 0.3315 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2904 Z= 0.133 Angle : 0.542 6.826 3963 Z= 0.267 Chirality : 0.038 0.125 447 Planarity : 0.004 0.039 476 Dihedral : 16.822 176.427 419 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.32 % Allowed : 9.57 % Favored : 89.11 % 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: 2.08 (0.49), residues: 342 helix: 2.64 (0.36), residues: 240 sheet: None (None), residues: 0 loop : -1.93 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.015 0.001 TYR A 85 PHE 0.011 0.001 PHE A 148 TRP 0.032 0.001 TRP A 86 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2903) covalent geometry : angle 0.54171 ( 3961) SS BOND : bond 0.00065 ( 1) SS BOND : angle 1.17966 ( 2) hydrogen bonds : bond 0.05103 ( 175) hydrogen bonds : angle 3.67238 ( 525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.073 Fit side-chains REVERT: A 277 SER cc_start: 0.8092 (t) cc_final: 0.7635 (p) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0431 time to fit residues: 1.6900 Evaluate side-chains 26 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127201 restraints weight = 3521.112| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.09 r_work: 0.3370 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2904 Z= 0.135 Angle : 0.529 7.008 3963 Z= 0.264 Chirality : 0.039 0.196 447 Planarity : 0.004 0.036 476 Dihedral : 14.213 171.471 419 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.65 % Allowed : 11.22 % Favored : 87.13 % 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: 2.20 (0.49), residues: 342 helix: 2.72 (0.36), residues: 240 sheet: None (None), residues: 0 loop : -1.84 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 40 TYR 0.014 0.001 TYR A 85 PHE 0.013 0.001 PHE A 223 TRP 0.023 0.001 TRP A 86 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2903) covalent geometry : angle 0.52798 ( 3961) SS BOND : bond 0.00043 ( 1) SS BOND : angle 1.19781 ( 2) hydrogen bonds : bond 0.05080 ( 175) hydrogen bonds : angle 3.46836 ( 525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.083 Fit side-chains REVERT: A 277 SER cc_start: 0.8119 (t) cc_final: 0.7653 (p) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.0409 time to fit residues: 1.7874 Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.156276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127615 restraints weight = 3441.053| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.06 r_work: 0.3334 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2904 Z= 0.127 Angle : 0.507 7.231 3963 Z= 0.255 Chirality : 0.038 0.143 447 Planarity : 0.004 0.039 476 Dihedral : 12.802 166.872 419 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.65 % Allowed : 12.54 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.25 (0.49), residues: 342 helix: 2.68 (0.36), residues: 242 sheet: None (None), residues: 0 loop : -1.70 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 40 TYR 0.012 0.001 TYR A 85 PHE 0.011 0.001 PHE A 223 TRP 0.015 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2903) covalent geometry : angle 0.50681 ( 3961) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.11788 ( 2) hydrogen bonds : bond 0.04835 ( 175) hydrogen bonds : angle 3.37818 ( 525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.112 Fit side-chains REVERT: A 277 SER cc_start: 0.7961 (t) cc_final: 0.7506 (p) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.0505 time to fit residues: 2.1944 Evaluate side-chains 32 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.0070 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.0040 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.2608 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.161438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133390 restraints weight = 3431.015| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.00 r_work: 0.3443 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2904 Z= 0.097 Angle : 0.465 7.266 3963 Z= 0.231 Chirality : 0.036 0.127 447 Planarity : 0.004 0.034 476 Dihedral : 12.171 168.560 419 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.33 % Allowed : 14.85 % Favored : 84.82 % 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: 2.48 (0.50), residues: 342 helix: 2.79 (0.36), residues: 244 sheet: None (None), residues: 0 loop : -1.53 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.011 0.001 TYR A 85 PHE 0.008 0.001 PHE A 148 TRP 0.010 0.001 TRP A 86 HIS 0.001 0.000 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 2903) covalent geometry : angle 0.46484 ( 3961) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.75566 ( 2) hydrogen bonds : bond 0.03832 ( 175) hydrogen bonds : angle 3.22639 ( 525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.123 Fit side-chains REVERT: A 277 SER cc_start: 0.7912 (t) cc_final: 0.7460 (p) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0532 time to fit residues: 1.8504 Evaluate side-chains 24 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 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 = 0.3713 r_free = 0.3713 target = 0.157378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128721 restraints weight = 3453.250| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.07 r_work: 0.3343 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2904 Z= 0.119 Angle : 0.495 7.189 3963 Z= 0.247 Chirality : 0.037 0.123 447 Planarity : 0.004 0.041 476 Dihedral : 12.046 165.712 419 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.98 % Allowed : 13.53 % Favored : 84.49 % 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: 2.47 (0.50), residues: 342 helix: 2.76 (0.36), residues: 244 sheet: None (None), residues: 0 loop : -1.44 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.009 0.001 TYR A 85 PHE 0.009 0.001 PHE A 223 TRP 0.013 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2903) covalent geometry : angle 0.49452 ( 3961) SS BOND : bond 0.00070 ( 1) SS BOND : angle 1.13853 ( 2) hydrogen bonds : bond 0.04600 ( 175) hydrogen bonds : angle 3.25245 ( 525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.107 Fit side-chains REVERT: A 195 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: A 277 SER cc_start: 0.7877 (t) cc_final: 0.7376 (p) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.0499 time to fit residues: 2.1486 Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 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 = 0.3701 r_free = 0.3701 target = 0.156285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127745 restraints weight = 3460.302| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.05 r_work: 0.3344 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2904 Z= 0.122 Angle : 0.506 7.205 3963 Z= 0.251 Chirality : 0.038 0.122 447 Planarity : 0.004 0.036 476 Dihedral : 11.868 164.347 419 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.98 % Allowed : 13.86 % Favored : 84.16 % 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: 2.45 (0.50), residues: 342 helix: 2.73 (0.36), residues: 244 sheet: None (None), residues: 0 loop : -1.43 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.010 0.001 TYR A 85 PHE 0.008 0.001 PHE A 223 TRP 0.013 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2903) covalent geometry : angle 0.50560 ( 3961) SS BOND : bond 0.00069 ( 1) SS BOND : angle 1.07368 ( 2) hydrogen bonds : bond 0.04714 ( 175) hydrogen bonds : angle 3.27436 ( 525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.107 Fit side-chains REVERT: A 195 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: A 277 SER cc_start: 0.7912 (t) cc_final: 0.7440 (p) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.0479 time to fit residues: 2.0261 Evaluate side-chains 31 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.156925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128422 restraints weight = 3483.243| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.06 r_work: 0.3344 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2904 Z= 0.113 Angle : 0.495 7.201 3963 Z= 0.245 Chirality : 0.037 0.122 447 Planarity : 0.004 0.038 476 Dihedral : 11.767 163.711 419 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.32 % Allowed : 14.85 % Favored : 83.83 % 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: 2.49 (0.50), residues: 342 helix: 2.76 (0.36), residues: 244 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.009 0.001 TYR A 85 PHE 0.008 0.001 PHE A 148 TRP 0.011 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 2903) covalent geometry : angle 0.49482 ( 3961) SS BOND : bond 0.00039 ( 1) SS BOND : angle 1.01754 ( 2) hydrogen bonds : bond 0.04504 ( 175) hydrogen bonds : angle 3.23803 ( 525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.069 Fit side-chains REVERT: A 195 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: A 277 SER cc_start: 0.7812 (t) cc_final: 0.7374 (p) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0391 time to fit residues: 1.5160 Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.154428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126395 restraints weight = 3545.791| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.00 r_work: 0.3324 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2904 Z= 0.134 Angle : 0.524 7.181 3963 Z= 0.260 Chirality : 0.038 0.123 447 Planarity : 0.004 0.040 476 Dihedral : 11.764 161.349 419 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.98 % Allowed : 14.52 % Favored : 83.50 % 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: 2.51 (0.50), residues: 342 helix: 2.76 (0.36), residues: 242 sheet: None (None), residues: 0 loop : -1.24 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR A 85 PHE 0.009 0.001 PHE A 223 TRP 0.013 0.001 TRP A 86 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2903) covalent geometry : angle 0.52298 ( 3961) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.24492 ( 2) hydrogen bonds : bond 0.05036 ( 175) hydrogen bonds : angle 3.30469 ( 525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.108 Fit side-chains REVERT: A 195 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: A 256 THR cc_start: 0.8380 (t) cc_final: 0.7908 (p) REVERT: A 277 SER cc_start: 0.7989 (t) cc_final: 0.7525 (p) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.0461 time to fit residues: 2.0349 Evaluate side-chains 31 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 13 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.156668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128518 restraints weight = 3574.960| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.02 r_work: 0.3343 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2904 Z= 0.111 Angle : 0.500 7.219 3963 Z= 0.246 Chirality : 0.037 0.122 447 Planarity : 0.004 0.036 476 Dihedral : 11.667 161.570 419 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.99 % Allowed : 16.17 % Favored : 82.84 % 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: 2.56 (0.50), residues: 342 helix: 2.80 (0.36), residues: 242 sheet: None (None), residues: 0 loop : -1.25 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.009 0.001 TYR A 85 PHE 0.008 0.001 PHE A 309 TRP 0.011 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2903) covalent geometry : angle 0.49979 ( 3961) SS BOND : bond 0.00030 ( 1) SS BOND : angle 1.01424 ( 2) hydrogen bonds : bond 0.04497 ( 175) hydrogen bonds : angle 3.24746 ( 525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.104 Fit side-chains REVERT: A 195 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 277 SER cc_start: 0.7839 (t) cc_final: 0.7420 (p) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.0465 time to fit residues: 1.8575 Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.156379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128610 restraints weight = 3472.945| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.98 r_work: 0.3343 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2904 Z= 0.114 Angle : 0.504 7.248 3963 Z= 0.248 Chirality : 0.037 0.122 447 Planarity : 0.004 0.038 476 Dihedral : 11.653 160.963 419 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.98 % Allowed : 15.84 % Favored : 82.18 % 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: 2.61 (0.50), residues: 342 helix: 2.82 (0.36), residues: 242 sheet: None (None), residues: 0 loop : -1.18 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.010 0.001 TYR A 85 PHE 0.008 0.001 PHE A 148 TRP 0.011 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 2903) covalent geometry : angle 0.50402 ( 3961) SS BOND : bond 0.00054 ( 1) SS BOND : angle 1.04388 ( 2) hydrogen bonds : bond 0.04533 ( 175) hydrogen bonds : angle 3.24392 ( 525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 777.54 seconds wall clock time: 14 minutes 3.11 seconds (843.11 seconds total)