Starting phenix.real_space_refine on Wed Mar 5 16:23:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3m_44145/03_2025/9b3m_44145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3m_44145/03_2025/9b3m_44145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3m_44145/03_2025/9b3m_44145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3m_44145/03_2025/9b3m_44145.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3m_44145/03_2025/9b3m_44145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3m_44145/03_2025/9b3m_44145.cif" } resolution = 3.21 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 14 5.16 5 C 1799 2.51 5 N 411 2.21 5 O 445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2669 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2669 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 2 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 3.97, per 1000 atoms: 1.49 Number of scatterers: 2669 At special positions: 0 Unit cell: (61.05, 70.95, 78.375, 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 14 16.00 O 445 8.00 N 411 7.00 C 1799 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: 0.85 Conformation dependent library (CDL) restraints added in 469.6 milliseconds 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 656 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 95.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 removed outlier: 3.588A pdb=" N PHE A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.206A pdb=" N VAL A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Proline residue: A 27 - end of helix Processing helix chain 'A' and resid 36 through 65 Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 67 through 88 Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 124 through 154 removed outlier: 3.740A pdb=" N ASN A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.926A pdb=" N PHE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 177 Processing helix chain 'A' and resid 200 through 234 removed outlier: 4.142A pdb=" N PHE A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.638A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 5.367A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 288 removed outlier: 3.599A pdb=" N PHE A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 321 removed outlier: 4.258A pdb=" N PHE A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 325 through 354 Proline residue: A 344 - end of helix removed outlier: 3.900A pdb=" N ASP A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 388 removed outlier: 3.512A pdb=" N ASP A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 747 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: 0.91 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 400 1.31 - 1.43: 764 1.43 - 1.56: 1544 1.56 - 1.68: 0 1.68 - 1.80: 27 Bond restraints: 2735 Sorted by residual: bond pdb=" C GLY A 59 " pdb=" N THR A 60 " ideal model delta sigma weight residual 1.334 1.287 0.048 1.27e-02 6.20e+03 1.41e+01 bond pdb=" C TYR A 131 " pdb=" O TYR A 131 " ideal model delta sigma weight residual 1.236 1.187 0.048 1.29e-02 6.01e+03 1.39e+01 bond pdb=" CA SER A 133 " pdb=" CB SER A 133 " ideal model delta sigma weight residual 1.530 1.469 0.061 1.87e-02 2.86e+03 1.06e+01 bond pdb=" C GLY A 130 " pdb=" O GLY A 130 " ideal model delta sigma weight residual 1.235 1.273 -0.039 1.35e-02 5.49e+03 8.25e+00 bond pdb=" C ALA A 134 " pdb=" N ILE A 135 " ideal model delta sigma weight residual 1.334 1.299 0.034 1.26e-02 6.30e+03 7.43e+00 ... (remaining 2730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3628 1.90 - 3.81: 53 3.81 - 5.71: 26 5.71 - 7.62: 9 7.62 - 9.52: 3 Bond angle restraints: 3719 Sorted by residual: angle pdb=" N TYR A 131 " pdb=" CA TYR A 131 " pdb=" C TYR A 131 " ideal model delta sigma weight residual 112.54 103.65 8.89 1.22e+00 6.72e-01 5.31e+01 angle pdb=" C ILE A 136 " pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 120.29 110.77 9.52 1.42e+00 4.96e-01 4.50e+01 angle pdb=" C GLY A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 120.44 111.78 8.66 1.30e+00 5.92e-01 4.44e+01 angle pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " pdb=" CG ASN A 137 " ideal model delta sigma weight residual 112.60 106.49 6.11 1.00e+00 1.00e+00 3.74e+01 angle pdb=" N THR A 60 " pdb=" CA THR A 60 " pdb=" C THR A 60 " ideal model delta sigma weight residual 111.07 105.51 5.56 1.07e+00 8.73e-01 2.70e+01 ... (remaining 3714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1299 15.91 - 31.82: 180 31.82 - 47.73: 52 47.73 - 63.63: 15 63.63 - 79.54: 1 Dihedral angle restraints: 1547 sinusoidal: 516 harmonic: 1031 Sorted by residual: dihedral pdb=" C ASN A 137 " pdb=" N ASN A 137 " pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " ideal model delta harmonic sigma weight residual -122.60 -132.33 9.73 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" N ASN A 137 " pdb=" C ASN A 137 " pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " ideal model delta harmonic sigma weight residual 122.80 131.20 -8.40 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA VAL A 175 " pdb=" C VAL A 175 " pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 1544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 407 0.067 - 0.135: 35 0.135 - 0.202: 2 0.202 - 0.269: 0 0.269 - 0.336: 1 Chirality restraints: 445 Sorted by residual: chirality pdb=" CA ASN A 137 " pdb=" N ASN A 137 " pdb=" C ASN A 137 " pdb=" CB ASN A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ALA A 134 " pdb=" N ALA A 134 " pdb=" C ALA A 134 " pdb=" CB ALA A 134 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE A 136 " pdb=" CA ILE A 136 " pdb=" CG1 ILE A 136 " pdb=" CG2 ILE A 136 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 442 not shown) Planarity restraints: 454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 128 " 0.024 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C ASN A 128 " -0.081 2.00e-02 2.50e+03 pdb=" O ASN A 128 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A 129 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 134 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C ALA A 134 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 134 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 135 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 131 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C TYR A 131 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR A 131 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 132 " 0.012 2.00e-02 2.50e+03 ... (remaining 451 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 417 2.75 - 3.29: 2753 3.29 - 3.83: 4782 3.83 - 4.36: 4899 4.36 - 4.90: 9038 Nonbonded interactions: 21889 Sorted by model distance: nonbonded pdb=" OD1 ASP A 239 " pdb=" OH TYR A 292 " model vdw 2.215 3.040 nonbonded pdb=" O GLN A 378 " pdb=" NE2 GLN A 378 " model vdw 2.281 3.120 nonbonded pdb=" O THR A 60 " pdb=" N ASP A 63 " model vdw 2.291 3.120 nonbonded pdb=" O SER A 241 " pdb=" OG1 THR A 245 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 228 " pdb=" NZ LYS A 232 " model vdw 2.377 3.120 ... (remaining 21884 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: 3.110 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.004 0.061 2735 Z= 0.269 Angle : 0.756 9.523 3719 Z= 0.477 Chirality : 0.042 0.336 445 Planarity : 0.005 0.047 454 Dihedral : 16.771 79.541 891 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.33 % Allowed : 33.07 % Favored : 64.59 % Cbeta Deviations : 0.30 % 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: 2.89 (0.46), residues: 359 helix: 2.28 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.18 (1.03), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.010 0.001 PHE A 335 TYR 0.009 0.001 TYR A 228 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.280 Fit side-chains REVERT: A 129 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (t80) REVERT: A 241 SER cc_start: 0.8471 (t) cc_final: 0.8195 (p) REVERT: A 338 MET cc_start: 0.8036 (tpt) cc_final: 0.7543 (tpt) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.1446 time to fit residues: 12.2067 Evaluate side-chains 69 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 295 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.153469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127379 restraints weight = 3861.861| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.85 r_work: 0.3409 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2735 Z= 0.296 Angle : 0.565 8.581 3719 Z= 0.291 Chirality : 0.038 0.123 445 Planarity : 0.004 0.038 454 Dihedral : 6.670 59.875 387 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 6.23 % Allowed : 31.13 % Favored : 62.65 % 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: 2.85 (0.45), residues: 359 helix: 2.18 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.27 (1.11), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.017 0.002 PHE A 259 TYR 0.015 0.001 TYR A 228 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.303 Fit side-chains REVERT: A 149 PHE cc_start: 0.8066 (m-80) cc_final: 0.7587 (m-80) REVERT: A 338 MET cc_start: 0.8088 (tpt) cc_final: 0.7746 (tpt) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.1410 time to fit residues: 12.7450 Evaluate side-chains 73 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.153353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127445 restraints weight = 3867.147| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.84 r_work: 0.3412 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2735 Z= 0.264 Angle : 0.537 8.770 3719 Z= 0.275 Chirality : 0.037 0.123 445 Planarity : 0.003 0.037 454 Dihedral : 6.302 56.455 385 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 7.00 % Allowed : 28.79 % Favored : 64.20 % 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: 2.94 (0.44), residues: 359 helix: 2.24 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -1.24 (1.10), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.010 0.001 PHE A 335 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.258 Fit side-chains REVERT: A 338 MET cc_start: 0.8132 (tpt) cc_final: 0.7845 (tpt) outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 0.1403 time to fit residues: 13.2063 Evaluate side-chains 77 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126770 restraints weight = 3890.069| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.85 r_work: 0.3403 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2735 Z= 0.283 Angle : 0.548 8.921 3719 Z= 0.278 Chirality : 0.038 0.136 445 Planarity : 0.003 0.039 454 Dihedral : 6.250 55.370 385 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 6.23 % Allowed : 31.13 % Favored : 62.65 % 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: 3.02 (0.45), residues: 359 helix: 2.27 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.84 (1.11), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.010 0.001 PHE A 335 TYR 0.014 0.001 TYR A 228 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.295 Fit side-chains REVERT: A 338 MET cc_start: 0.8146 (tpt) cc_final: 0.7890 (tpt) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.1320 time to fit residues: 12.3137 Evaluate side-chains 75 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 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 = 0.3827 r_free = 0.3827 target = 0.153689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127266 restraints weight = 3915.884| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.87 r_work: 0.3410 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2735 Z= 0.252 Angle : 0.543 8.764 3719 Z= 0.276 Chirality : 0.037 0.122 445 Planarity : 0.003 0.038 454 Dihedral : 5.573 52.454 383 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 8.17 % Allowed : 29.96 % Favored : 61.87 % 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: 2.99 (0.44), residues: 359 helix: 2.25 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.84 (1.11), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.011 0.001 PHE A 140 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.302 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 82 average time/residue: 0.1311 time to fit residues: 13.1491 Evaluate side-chains 80 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 317 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.153094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126639 restraints weight = 3959.014| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.86 r_work: 0.3401 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2735 Z= 0.280 Angle : 0.576 8.987 3719 Z= 0.289 Chirality : 0.037 0.123 445 Planarity : 0.003 0.039 454 Dihedral : 5.546 50.635 383 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 8.17 % Allowed : 29.57 % Favored : 62.26 % 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: 2.90 (0.45), residues: 359 helix: 2.20 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.20 (1.08), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.010 0.001 PHE A 335 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.298 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 82 average time/residue: 0.1296 time to fit residues: 12.8675 Evaluate side-chains 80 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 317 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.0020 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.2366 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.156547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130083 restraints weight = 4026.068| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.91 r_work: 0.3442 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2735 Z= 0.184 Angle : 0.544 7.890 3719 Z= 0.270 Chirality : 0.036 0.117 445 Planarity : 0.003 0.039 454 Dihedral : 5.382 48.453 383 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 7.00 % Allowed : 30.74 % Favored : 62.26 % 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: 3.19 (0.45), residues: 359 helix: 2.38 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.76 (1.12), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.011 0.001 PHE A 335 TYR 0.011 0.001 TYR A 228 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.264 Fit side-chains REVERT: A 81 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7666 (p) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.1307 time to fit residues: 12.7829 Evaluate side-chains 83 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 1 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129252 restraints weight = 3921.330| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.87 r_work: 0.3426 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2735 Z= 0.204 Angle : 0.553 8.279 3719 Z= 0.273 Chirality : 0.036 0.117 445 Planarity : 0.003 0.039 454 Dihedral : 5.309 47.708 383 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 7.00 % Allowed : 30.35 % Favored : 62.65 % 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: 3.18 (0.45), residues: 359 helix: 2.38 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.14 (1.11), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.010 0.001 PHE A 140 TYR 0.011 0.001 TYR A 228 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.299 Fit side-chains REVERT: A 81 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7677 (p) outliers start: 18 outliers final: 15 residues processed: 85 average time/residue: 0.1400 time to fit residues: 14.3600 Evaluate side-chains 88 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 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 = 0.3834 r_free = 0.3834 target = 0.154348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127766 restraints weight = 3988.053| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.88 r_work: 0.3405 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2735 Z= 0.262 Angle : 0.588 8.726 3719 Z= 0.291 Chirality : 0.037 0.135 445 Planarity : 0.003 0.038 454 Dihedral : 5.326 46.707 383 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 5.84 % Allowed : 31.13 % Favored : 63.04 % 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: 3.10 (0.45), residues: 359 helix: 2.31 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.66 (1.10), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.010 0.001 PHE A 78 TYR 0.013 0.001 TYR A 225 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.268 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.1497 time to fit residues: 13.1841 Evaluate side-chains 79 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 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 = 0.3827 r_free = 0.3827 target = 0.153570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126618 restraints weight = 4002.239| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.90 r_work: 0.3393 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2735 Z= 0.277 Angle : 0.604 8.950 3719 Z= 0.299 Chirality : 0.038 0.131 445 Planarity : 0.004 0.039 454 Dihedral : 5.329 46.208 383 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 5.84 % Allowed : 31.91 % Favored : 62.26 % 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: 3.01 (0.45), residues: 359 helix: 2.25 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.78 (1.13), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.012 0.001 PHE A 140 TYR 0.012 0.001 TYR A 228 ARG 0.001 0.000 ARG A 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.273 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.1474 time to fit residues: 12.8012 Evaluate side-chains 76 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 32 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.155342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128831 restraints weight = 3926.977| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.88 r_work: 0.3417 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2735 Z= 0.222 Angle : 0.583 8.237 3719 Z= 0.288 Chirality : 0.037 0.118 445 Planarity : 0.003 0.039 454 Dihedral : 5.272 45.475 383 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 5.06 % Allowed : 31.52 % Favored : 63.42 % 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: 3.11 (0.45), residues: 359 helix: 2.31 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.74 (1.19), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.012 0.001 PHE A 140 TYR 0.013 0.001 TYR A 225 ARG 0.001 0.000 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.04 seconds wall clock time: 33 minutes 25.60 seconds (2005.60 seconds total)