Starting phenix.real_space_refine on Sat Apr 26 17:13:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3o_44147/04_2025/9b3o_44147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3o_44147/04_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_44147/04_2025/9b3o_44147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3o_44147/04_2025/9b3o_44147.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3o_44147/04_2025/9b3o_44147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3o_44147/04_2025/9b3o_44147.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 3.10, per 1000 atoms: 1.18 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: 0.80 Conformation dependent library (CDL) restraints added in 380.7 milliseconds 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: 0.22 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: 0.67 Time building geometry restraints manager: 0.94 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.050 Process input model: 13.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (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 TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.014 0.001 PHE A 47 TYR 0.007 0.001 TYR A 292 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.11154 ( 244) hydrogen bonds : angle 4.77004 ( 732) covalent geometry : bond 0.00328 ( 2694) covalent geometry : angle 0.60418 ( 3665) *********************** 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 : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1331 time to fit residues: 9.3101 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.138366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112679 restraints weight = 3987.035| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.86 r_work: 0.3261 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2694 Z= 0.163 Angle : 0.572 8.120 3665 Z= 0.287 Chirality : 0.038 0.130 440 Planarity : 0.004 0.039 448 Dihedral : 3.793 17.530 374 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 32.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.46), residues: 355 helix: 2.05 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.70 (0.93), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 379 PHE 0.014 0.002 PHE A 47 TYR 0.009 0.001 TYR A 278 ARG 0.002 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 244) hydrogen bonds : angle 3.68181 ( 732) covalent geometry : bond 0.00395 ( 2694) covalent geometry : angle 0.57191 ( 3665) *********************** 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 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.280 Fit side-chains REVERT: A 324 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6679 (mtp85) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.1106 time to fit residues: 9.2254 Evaluate side-chains 61 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113738 restraints weight = 3987.577| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.78 r_work: 0.3274 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.004 0.038 2694 Z= 0.146 Angle : 0.554 8.050 3665 Z= 0.275 Chirality : 0.038 0.127 440 Planarity : 0.004 0.038 448 Dihedral : 3.810 17.688 374 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 29.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.46), residues: 355 helix: 2.12 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.60 (0.94), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.013 0.001 PHE A 47 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 244) hydrogen bonds : angle 3.58371 ( 732) covalent geometry : bond 0.00358 ( 2694) covalent geometry : angle 0.55401 ( 3665) *********************** 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: 11 poor density : 58 time to evaluate : 0.294 Fit side-chains REVERT: A 8 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 266 PHE cc_start: 0.7655 (m-10) cc_final: 0.7417 (m-80) REVERT: A 324 ARG cc_start: 0.7049 (mmt180) cc_final: 0.6697 (mtp85) outliers start: 11 outliers final: 4 residues processed: 66 average time/residue: 0.1018 time to fit residues: 8.6019 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 : 0.291 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113877 restraints weight = 3989.850| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.75 r_work: 0.3244 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2694 Z= 0.158 Angle : 0.567 8.108 3665 Z= 0.279 Chirality : 0.039 0.139 440 Planarity : 0.004 0.037 448 Dihedral : 3.818 17.614 374 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.02 % Allowed : 31.33 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.46), residues: 355 helix: 2.11 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.59 (0.96), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.014 0.001 PHE A 47 TYR 0.011 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 244) hydrogen bonds : angle 3.63203 ( 732) covalent geometry : bond 0.00389 ( 2694) covalent geometry : angle 0.56689 ( 3665) *********************** 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 70 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.313 Fit side-chains REVERT: A 8 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8381 (mp) REVERT: A 65 LEU cc_start: 0.6452 (mp) cc_final: 0.6150 (tt) REVERT: A 324 ARG cc_start: 0.7124 (mmt180) cc_final: 0.6779 (mtp85) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1199 time to fit residues: 10.2312 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 : 0.317 ------------------------------------------------------------------------------- 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 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 0 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 = 0.3751 r_free = 0.3751 target = 0.140816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116793 restraints weight = 3953.576| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.81 r_work: 0.3343 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2694 Z= 0.151 Angle : 0.561 7.754 3665 Z= 0.277 Chirality : 0.038 0.145 440 Planarity : 0.004 0.036 448 Dihedral : 3.800 17.532 374 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 32.13 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.46), residues: 355 helix: 2.16 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.54 (0.96), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.015 0.001 PHE A 327 TYR 0.017 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 244) hydrogen bonds : angle 3.60410 ( 732) covalent geometry : bond 0.00368 ( 2694) covalent geometry : angle 0.56118 ( 3665) *********************** 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 68 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.270 Fit side-chains REVERT: A 8 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8351 (mp) REVERT: A 324 ARG cc_start: 0.7151 (mmt180) cc_final: 0.6778 (mtp85) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.1106 time to fit residues: 9.1865 Evaluate side-chains 66 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 239 ASP 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 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.140994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116975 restraints weight = 4040.330| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.82 r_work: 0.3343 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1227 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 : 0.553 7.319 3665 Z= 0.274 Chirality : 0.038 0.151 440 Planarity : 0.004 0.036 448 Dihedral : 3.790 17.587 374 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.82 % Allowed : 30.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.46), residues: 355 helix: 2.15 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.64 (0.97), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.017 0.001 PHE A 170 TYR 0.012 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 244) hydrogen bonds : angle 3.59188 ( 732) covalent geometry : bond 0.00354 ( 2694) covalent geometry : angle 0.55327 ( 3665) *********************** 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 : 0.293 Fit side-chains REVERT: A 324 ARG cc_start: 0.7137 (mmt180) cc_final: 0.6794 (mtp85) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1036 time to fit residues: 8.8115 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE 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 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 6 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112733 restraints weight = 4171.485| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.86 r_work: 0.3244 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2694 Z= 0.162 Angle : 0.583 7.437 3665 Z= 0.286 Chirality : 0.039 0.150 440 Planarity : 0.004 0.036 448 Dihedral : 3.828 17.248 374 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.46), residues: 355 helix: 2.13 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.69 (0.96), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.026 0.002 PHE A 170 TYR 0.017 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 244) hydrogen bonds : angle 3.65633 ( 732) covalent geometry : bond 0.00399 ( 2694) covalent geometry : angle 0.58321 ( 3665) *********************** 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 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.277 Fit side-chains REVERT: A 324 ARG cc_start: 0.7170 (mmt180) cc_final: 0.6806 (mtp85) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.1047 time to fit residues: 8.6014 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 : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.141870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117836 restraints weight = 3950.694| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.82 r_work: 0.3359 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1287 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= 0.133 Angle : 0.589 10.293 3665 Z= 0.280 Chirality : 0.039 0.150 440 Planarity : 0.004 0.036 448 Dihedral : 3.757 16.674 374 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 31.73 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.46), residues: 355 helix: 2.19 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.61 (0.99), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.011 0.001 PHE A 47 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 244) hydrogen bonds : angle 3.56910 ( 732) covalent geometry : bond 0.00318 ( 2694) covalent geometry : angle 0.58858 ( 3665) *********************** 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 66 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.303 Fit side-chains REVERT: A 324 ARG cc_start: 0.7120 (mmt180) cc_final: 0.6785 (mtp85) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.1086 time to fit residues: 8.9947 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115955 restraints weight = 4023.016| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.85 r_work: 0.3343 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1342 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= 0.147 Angle : 0.601 9.900 3665 Z= 0.286 Chirality : 0.039 0.149 440 Planarity : 0.004 0.036 448 Dihedral : 3.777 16.472 374 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.46), residues: 355 helix: 2.18 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.74 (0.95), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.023 0.002 PHE A 170 TYR 0.016 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 244) hydrogen bonds : angle 3.63529 ( 732) covalent geometry : bond 0.00356 ( 2694) covalent geometry : angle 0.60112 ( 3665) *********************** 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 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.271 Fit side-chains REVERT: A 324 ARG cc_start: 0.7143 (mmt180) cc_final: 0.6797 (mtp85) outliers start: 9 outliers final: 9 residues processed: 64 average time/residue: 0.1026 time to fit residues: 8.4078 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 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 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 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.141899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118144 restraints weight = 4013.080| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.83 r_work: 0.3356 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2694 Z= 0.134 Angle : 0.590 10.021 3665 Z= 0.282 Chirality : 0.038 0.150 440 Planarity : 0.004 0.036 448 Dihedral : 3.732 16.322 374 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 32.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.46), residues: 355 helix: 2.21 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.47 (0.94), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.017 0.001 PHE A 170 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 244) hydrogen bonds : angle 3.57456 ( 732) covalent geometry : bond 0.00320 ( 2694) covalent geometry : angle 0.58994 ( 3665) ********************** 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 68 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.301 Fit side-chains REVERT: A 157 MET cc_start: 0.7990 (tpt) cc_final: 0.7639 (tpp) REVERT: A 324 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6764 (mtp85) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.1094 time to fit residues: 9.1786 Evaluate side-chains 66 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 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 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 26 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.138329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113753 restraints weight = 3922.923| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.79 r_work: 0.3267 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2694 Z= 0.145 Angle : 0.600 9.857 3665 Z= 0.287 Chirality : 0.039 0.148 440 Planarity : 0.004 0.036 448 Dihedral : 3.760 16.980 374 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 32.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.46), residues: 355 helix: 2.19 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.54 (0.92), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.026 0.002 PHE A 327 TYR 0.036 0.002 TYR A 228 ARG 0.001 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 244) hydrogen bonds : angle 3.61778 ( 732) covalent geometry : bond 0.00351 ( 2694) covalent geometry : angle 0.60012 ( 3665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.74 seconds wall clock time: 32 minutes 6.65 seconds (1926.65 seconds total)