Starting phenix.real_space_refine on Wed Sep 17 03:15:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3o_44147/09_2025/9b3o_44147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3o_44147/09_2025/9b3o_44147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3o_44147/09_2025/9b3o_44147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3o_44147/09_2025/9b3o_44147.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3o_44147/09_2025/9b3o_44147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3o_44147/09_2025/9b3o_44147.cif" } resolution = 3.18 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= 0.038 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 15 5.16 5 C 1770 2.51 5 N 406 2.21 5 O 439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2630 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2630 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 12, 'TRANS': 350} Chain breaks: 3 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 0.98, per 1000 atoms: 0.37 Number of scatterers: 2630 At special positions: 0 Unit cell: (60.225, 69.3, 80.85, 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 15 16.00 O 439 8.00 N 406 7.00 C 1770 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: 0.24 Conformation dependent library (CDL) restraints added in 86.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 4.052A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 4.217A pdb=" N VAL A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.897A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.984A pdb=" N CYS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 119 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 127 through 152 Proline residue: A 144 - end of helix removed outlier: 3.716A pdb=" N GLU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.705A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 6.384A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 288 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.678A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 321 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 356 through 390 244 hydrogen bonds defined for protein. 732 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: 0.40 Time building geometry restraints manager: 0.32 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: 784 1.34 - 1.46: 651 1.46 - 1.58: 1230 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 2694 Sorted by residual: bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.34e-01 bond pdb=" CG PRO A 311 " pdb=" CD PRO A 311 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.96e-01 bond pdb=" CB PRO A 207 " pdb=" CG PRO A 207 " ideal model delta sigma weight residual 1.492 1.462 0.030 5.00e-02 4.00e+02 3.66e-01 bond pdb=" C PHE A 306 " pdb=" O PHE A 306 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.19e-02 7.06e+03 3.63e-01 bond pdb=" CG PRO A 121 " pdb=" CD PRO A 121 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.47e-01 ... (remaining 2689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3607 1.78 - 3.56: 39 3.56 - 5.34: 13 5.34 - 7.13: 3 7.13 - 8.91: 3 Bond angle restraints: 3665 Sorted by residual: angle pdb=" C GLY A 66 " pdb=" N LYS A 67 " pdb=" CA LYS A 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " pdb=" CG LEU A 65 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" CA LEU A 386 " pdb=" CB LEU A 386 " pdb=" CG LEU A 386 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.58e+00 angle pdb=" CB MET A 95 " pdb=" CG MET A 95 " pdb=" SD MET A 95 " ideal model delta sigma weight residual 112.70 119.32 -6.62 3.00e+00 1.11e-01 4.88e+00 angle pdb=" CA LEU A 69 " pdb=" CB LEU A 69 " pdb=" CG LEU A 69 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.64e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 1248 14.04 - 28.07: 177 28.07 - 42.11: 68 42.11 - 56.14: 22 56.14 - 70.18: 5 Dihedral angle restraints: 1520 sinusoidal: 498 harmonic: 1022 Sorted by residual: dihedral pdb=" CA LYS A 67 " pdb=" C LYS A 67 " pdb=" N LYS A 68 " pdb=" CA LYS A 68 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS A 64 " pdb=" C LYS A 64 " pdb=" N LEU A 65 " pdb=" CA LEU A 65 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " pdb=" CG ARG A 98 " pdb=" CD ARG A 98 " ideal model delta sinusoidal sigma weight residual -60.00 -119.91 59.91 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 269 0.025 - 0.050: 90 0.050 - 0.075: 50 0.075 - 0.100: 27 0.100 - 0.125: 4 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" C PRO A 144 " pdb=" CB PRO A 144 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 437 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 212 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU A 212 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 212 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 213 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 343 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 344 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 211 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.95e+00 pdb=" C THR A 211 " 0.024 2.00e-02 2.50e+03 pdb=" O THR A 211 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 212 " -0.008 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 810 2.82 - 3.34: 2787 3.34 - 3.86: 4536 3.86 - 4.38: 4895 4.38 - 4.90: 8587 Nonbonded interactions: 21615 Sorted by model distance: nonbonded pdb=" O LEU A 30 " pdb=" N LEU A 35 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASN A 137 " pdb=" NE ARG A 310 " model vdw 2.306 3.120 nonbonded pdb=" O GLY A 101 " pdb=" OG SER A 104 " model vdw 2.314 3.040 nonbonded pdb=" O ILE A 295 " pdb=" OG SER A 299 " model vdw 2.359 3.040 nonbonded pdb=" O ALA A 321 " pdb=" NE2 GLN A 325 " model vdw 2.368 3.120 ... (remaining 21610 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: 2.260 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 0.030 2694 Z= 0.142 Angle : 0.604 8.907 3665 Z= 0.299 Chirality : 0.038 0.125 440 Planarity : 0.004 0.038 448 Dihedral : 16.770 70.178 868 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 34.14 % Favored : 65.86 % 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: 2.11 (0.46), residues: 355 helix: 1.93 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -3.86 (0.78), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.007 0.001 TYR A 292 PHE 0.014 0.001 PHE A 47 TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2694) covalent geometry : angle 0.60418 ( 3665) hydrogen bonds : bond 0.11154 ( 244) hydrogen bonds : angle 4.77004 ( 732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0545 time to fit residues: 3.8532 Evaluate side-chains 56 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.139952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115121 restraints weight = 3974.159| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.76 r_work: 0.3302 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2694 Z= 0.130 Angle : 0.553 8.165 3665 Z= 0.275 Chirality : 0.038 0.126 440 Planarity : 0.004 0.039 448 Dihedral : 3.733 17.279 374 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.21 % Allowed : 31.73 % Favored : 65.06 % 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: 2.53 (0.46), residues: 355 helix: 2.12 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.61 (0.95), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.007 0.001 TYR A 278 PHE 0.012 0.001 PHE A 47 TRP 0.007 0.001 TRP A 201 HIS 0.001 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2694) covalent geometry : angle 0.55347 ( 3665) hydrogen bonds : bond 0.03388 ( 244) hydrogen bonds : angle 3.57145 ( 732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.078 Fit side-chains REVERT: A 8 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 324 ARG cc_start: 0.6925 (mmt180) cc_final: 0.6605 (mtp85) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.0402 time to fit residues: 3.5203 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.140077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115286 restraints weight = 4021.451| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.77 r_work: 0.3291 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2694 Z= 0.137 Angle : 0.552 8.107 3665 Z= 0.272 Chirality : 0.038 0.127 440 Planarity : 0.004 0.038 448 Dihedral : 3.752 17.349 374 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 30.92 % Favored : 65.46 % 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: 2.58 (0.46), residues: 355 helix: 2.15 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.60 (0.95), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.013 0.001 TYR A 228 PHE 0.012 0.001 PHE A 47 TRP 0.008 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2694) covalent geometry : angle 0.55248 ( 3665) hydrogen bonds : bond 0.03377 ( 244) hydrogen bonds : angle 3.53420 ( 732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.094 Fit side-chains REVERT: A 8 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 324 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6626 (mtp85) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.0434 time to fit residues: 3.7957 Evaluate side-chains 64 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113723 restraints weight = 3987.580| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.75 r_work: 0.3265 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2694 Z= 0.166 Angle : 0.565 7.894 3665 Z= 0.281 Chirality : 0.039 0.139 440 Planarity : 0.004 0.037 448 Dihedral : 3.823 17.267 374 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 31.33 % Favored : 64.26 % 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 (0.46), residues: 355 helix: 2.10 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.78 (0.96), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.011 0.001 TYR A 228 PHE 0.014 0.001 PHE A 47 TRP 0.009 0.001 TRP A 201 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2694) covalent geometry : angle 0.56548 ( 3665) hydrogen bonds : bond 0.03557 ( 244) hydrogen bonds : angle 3.64728 ( 732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.090 Fit side-chains REVERT: A 8 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 65 LEU cc_start: 0.6457 (mp) cc_final: 0.6156 (tt) REVERT: A 324 ARG cc_start: 0.7102 (mmt180) cc_final: 0.6766 (mtp85) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.0449 time to fit residues: 3.8189 Evaluate side-chains 65 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116383 restraints weight = 3947.406| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.81 r_work: 0.3340 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2694 Z= 0.154 Angle : 0.560 7.581 3665 Z= 0.278 Chirality : 0.039 0.144 440 Planarity : 0.004 0.036 448 Dihedral : 3.802 17.285 374 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.61 % Allowed : 33.33 % Favored : 63.05 % 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 (0.46), residues: 355 helix: 2.14 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.70 (0.97), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.009 0.001 TYR A 228 PHE 0.015 0.001 PHE A 327 TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2694) covalent geometry : angle 0.56035 ( 3665) hydrogen bonds : bond 0.03451 ( 244) hydrogen bonds : angle 3.63194 ( 732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.098 Fit side-chains REVERT: A 8 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 324 ARG cc_start: 0.7152 (mmt180) cc_final: 0.6790 (mtp85) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.0442 time to fit residues: 3.8413 Evaluate side-chains 65 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117288 restraints weight = 3962.713| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.81 r_work: 0.3343 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2694 Z= 0.148 Angle : 0.553 7.377 3665 Z= 0.275 Chirality : 0.039 0.150 440 Planarity : 0.004 0.036 448 Dihedral : 3.802 17.436 374 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.82 % Allowed : 30.92 % Favored : 64.26 % 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: 2.62 (0.46), residues: 355 helix: 2.17 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.66 (0.98), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.014 0.001 TYR A 228 PHE 0.017 0.001 PHE A 170 TRP 0.009 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2694) covalent geometry : angle 0.55306 ( 3665) hydrogen bonds : bond 0.03379 ( 244) hydrogen bonds : angle 3.61746 ( 732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.102 Fit side-chains REVERT: A 8 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 150 MET cc_start: 0.8316 (mtp) cc_final: 0.7984 (mtm) REVERT: A 265 TYR cc_start: 0.7905 (t80) cc_final: 0.7582 (t80) REVERT: A 324 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6739 (mtp85) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.0491 time to fit residues: 4.0933 Evaluate side-chains 63 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119283 restraints weight = 3984.926| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.81 r_work: 0.3346 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2694 Z= 0.145 Angle : 0.559 7.451 3665 Z= 0.275 Chirality : 0.038 0.150 440 Planarity : 0.004 0.036 448 Dihedral : 3.773 17.027 374 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.02 % Allowed : 30.52 % Favored : 65.46 % 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: 2.64 (0.46), residues: 355 helix: 2.19 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.72 (0.93), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.008 0.001 TYR A 228 PHE 0.012 0.001 PHE A 47 TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2694) covalent geometry : angle 0.55859 ( 3665) hydrogen bonds : bond 0.03319 ( 244) hydrogen bonds : angle 3.59791 ( 732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.096 Fit side-chains REVERT: A 8 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 150 MET cc_start: 0.8334 (mtp) cc_final: 0.7999 (mtm) REVERT: A 324 ARG cc_start: 0.7131 (mmt180) cc_final: 0.6778 (mtp85) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.0435 time to fit residues: 3.4416 Evaluate side-chains 60 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.141579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117547 restraints weight = 4013.826| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.84 r_work: 0.3348 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2694 Z= 0.137 Angle : 0.577 10.178 3665 Z= 0.275 Chirality : 0.038 0.149 440 Planarity : 0.004 0.035 448 Dihedral : 3.748 16.598 374 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 30.12 % Favored : 65.86 % 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: 2.71 (0.46), residues: 355 helix: 2.23 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.61 (0.96), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.010 0.001 TYR A 228 PHE 0.013 0.001 PHE A 47 TRP 0.011 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2694) covalent geometry : angle 0.57664 ( 3665) hydrogen bonds : bond 0.03236 ( 244) hydrogen bonds : angle 3.56598 ( 732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.098 Fit side-chains REVERT: A 8 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 150 MET cc_start: 0.8365 (mtp) cc_final: 0.8071 (mtm) REVERT: A 324 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6772 (mtp85) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.0448 time to fit residues: 3.4824 Evaluate side-chains 60 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 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 = 0.3687 r_free = 0.3687 target = 0.138551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113708 restraints weight = 4059.768| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.79 r_work: 0.3254 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2694 Z= 0.166 Angle : 0.599 9.767 3665 Z= 0.287 Chirality : 0.039 0.148 440 Planarity : 0.004 0.036 448 Dihedral : 3.834 17.150 374 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 30.52 % Favored : 65.86 % 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: 2.60 (0.46), residues: 355 helix: 2.16 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.74 (0.91), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.011 0.001 TYR A 228 PHE 0.013 0.001 PHE A 47 TRP 0.012 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 2694) covalent geometry : angle 0.59872 ( 3665) hydrogen bonds : bond 0.03484 ( 244) hydrogen bonds : angle 3.67501 ( 732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.101 Fit side-chains REVERT: A 8 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 150 MET cc_start: 0.8322 (mtp) cc_final: 0.7965 (mtm) REVERT: A 265 TYR cc_start: 0.7773 (t80) cc_final: 0.7471 (t80) REVERT: A 324 ARG cc_start: 0.7140 (mmt180) cc_final: 0.6795 (mtp85) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.0432 time to fit residues: 3.4923 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119902 restraints weight = 4036.912| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.84 r_work: 0.3355 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2694 Z= 0.138 Angle : 0.581 9.931 3665 Z= 0.280 Chirality : 0.038 0.150 440 Planarity : 0.004 0.035 448 Dihedral : 3.785 16.280 374 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.02 % Allowed : 30.92 % Favored : 65.06 % 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: 2.63 (0.46), residues: 355 helix: 2.19 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.75 (0.91), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.014 0.001 TYR A 228 PHE 0.026 0.001 PHE A 327 TRP 0.012 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2694) covalent geometry : angle 0.58122 ( 3665) hydrogen bonds : bond 0.03268 ( 244) hydrogen bonds : angle 3.59508 ( 732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.101 Fit side-chains REVERT: A 8 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 150 MET cc_start: 0.8366 (mtp) cc_final: 0.8039 (mtm) REVERT: A 265 TYR cc_start: 0.7841 (t80) cc_final: 0.7504 (t80) REVERT: A 324 ARG cc_start: 0.7105 (mmt180) cc_final: 0.6784 (mtp85) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.0448 time to fit residues: 3.5333 Evaluate side-chains 63 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.142125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118352 restraints weight = 3994.395| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.84 r_work: 0.3357 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2694 Z= 0.130 Angle : 0.582 9.918 3665 Z= 0.277 Chirality : 0.038 0.150 440 Planarity : 0.004 0.035 448 Dihedral : 3.722 16.204 374 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.42 % Allowed : 30.12 % Favored : 65.46 % 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: 2.69 (0.46), residues: 355 helix: 2.22 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.71 (0.95), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.013 0.001 TYR A 228 PHE 0.024 0.001 PHE A 327 TRP 0.012 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2694) covalent geometry : angle 0.58151 ( 3665) hydrogen bonds : bond 0.03176 ( 244) hydrogen bonds : angle 3.54747 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.16 seconds wall clock time: 16 minutes 56.45 seconds (1016.45 seconds total)