Starting phenix.real_space_refine on Wed Mar 5 23:29:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uv0_26808/03_2025/7uv0_26808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uv0_26808/03_2025/7uv0_26808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2025/7uv0_26808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2025/7uv0_26808.map" model { file = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2025/7uv0_26808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2025/7uv0_26808.cif" } resolution = 3.1 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= 0.001 sd= 0.081 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: 7 Type Number sf(0) Gaussians I 1 10.91 5 P 1 5.49 5 S 27 5.16 5 Na 2 4.78 5 C 2494 2.51 5 N 594 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3739 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 24, 'TRANS': 476} Chain breaks: 3 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' NA': 2, '3PH': 1, 'IOD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 3.39, per 1000 atoms: 0.90 Number of scatterers: 3784 At special positions: 0 Unit cell: (67.284, 85.44, 83.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 1 52.95 S 27 16.00 P 1 15.00 Na 2 11.00 O 665 8.00 N 594 7.00 C 2494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 454.4 milliseconds 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 13 through 36 removed outlier: 3.765A pdb=" N TYR A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.647A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.835A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 126 through 161 Proline residue: A 152 - end of helix removed outlier: 3.511A pdb=" N GLY A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 Processing helix chain 'A' and resid 191 through 213 Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.502A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 4.197A pdb=" N THR A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.603A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.546A pdb=" N GLY A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 338 through 370 removed outlier: 4.119A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 409 removed outlier: 3.543A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.740A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 546 removed outlier: 4.345A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 846 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: 1.02 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 638 1.33 - 1.45: 1013 1.45 - 1.57: 2172 1.57 - 1.70: 2 1.70 - 1.82: 42 Bond restraints: 3867 Sorted by residual: bond pdb=" O13 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.522 1.654 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" O11 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.703 1.644 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" O14 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.527 1.493 0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 3PH A 704 " pdb=" O11 3PH A 704 " ideal model delta sigma weight residual 1.385 1.410 -0.025 2.00e-02 2.50e+03 1.50e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 5197 2.01 - 4.01: 64 4.01 - 6.02: 9 6.02 - 8.03: 0 8.03 - 10.04: 2 Bond angle restraints: 5272 Sorted by residual: angle pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 113.84 123.88 -10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O13 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 115.01 104.99 10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA PRO A 512 " pdb=" C PRO A 512 " pdb=" N ALA A 513 " ideal model delta sigma weight residual 114.74 117.04 -2.30 1.03e+00 9.43e-01 4.97e+00 angle pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O13 3PH A 704 " ideal model delta sigma weight residual 115.12 109.29 5.83 3.00e+00 1.11e-01 3.78e+00 angle pdb=" O11 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 104.78 110.05 -5.27 3.00e+00 1.11e-01 3.08e+00 ... (remaining 5267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2016 15.89 - 31.78: 172 31.78 - 47.66: 33 47.66 - 63.55: 17 63.55 - 79.44: 3 Dihedral angle restraints: 2241 sinusoidal: 829 harmonic: 1412 Sorted by residual: dihedral pdb=" CA ASP A 309 " pdb=" C ASP A 309 " pdb=" N CYS A 310 " pdb=" CA CYS A 310 " ideal model delta harmonic sigma weight residual 180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.93e+00 dihedral pdb=" CA HIS A 273 " pdb=" C HIS A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA LEU A 436 " pdb=" CB LEU A 436 " pdb=" CG LEU A 436 " pdb=" CD1 LEU A 436 " ideal model delta sinusoidal sigma weight residual 60.00 117.14 -57.14 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 471 0.039 - 0.079: 137 0.079 - 0.118: 24 0.118 - 0.158: 1 0.158 - 0.197: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" C2 3PH A 704 " pdb=" C1 3PH A 704 " pdb=" C3 3PH A 704 " pdb=" O21 3PH A 704 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 631 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO A 58 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 372 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 373 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C PHE A 247 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 191 2.72 - 3.28: 4322 3.28 - 3.84: 6823 3.84 - 4.40: 8257 4.40 - 4.96: 14074 Nonbonded interactions: 33667 Sorted by model distance: nonbonded pdb=" O PHE A 125 " pdb=" OG SER A 126 " model vdw 2.160 3.040 nonbonded pdb=" OE1 GLN A 72 " pdb="NA NA A 702 " model vdw 2.201 2.470 nonbonded pdb=" OH TYR A 17 " pdb=" O THR A 160 " model vdw 2.261 3.040 nonbonded pdb=" O GLN A 414 " pdb=" OG1 THR A 418 " model vdw 2.338 3.040 nonbonded pdb=" O THR A 115 " pdb=" NE2 GLN A 267 " model vdw 2.343 3.120 ... (remaining 33662 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: 1.470 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.270 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.005 0.132 3867 Z= 0.291 Angle : 0.611 10.036 5272 Z= 0.307 Chirality : 0.037 0.197 634 Planarity : 0.005 0.055 639 Dihedral : 13.420 79.437 1346 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.51 % Allowed : 8.86 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.40), residues: 493 helix: 0.93 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -2.40 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 PHE 0.009 0.001 PHE A 304 TYR 0.008 0.001 TYR A 348 ARG 0.003 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.409 Fit side-chains REVERT: A 154 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 232 MET cc_start: 0.7860 (mmt) cc_final: 0.7589 (mmm) REVERT: A 269 TYR cc_start: 0.6461 (m-10) cc_final: 0.6194 (m-10) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1639 time to fit residues: 13.2586 Evaluate side-chains 57 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131731 restraints weight = 3326.819| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.20 r_work: 0.3537 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3867 Z= 0.295 Angle : 0.629 9.000 5272 Z= 0.315 Chirality : 0.040 0.140 634 Planarity : 0.005 0.058 639 Dihedral : 9.569 60.469 576 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.04 % Allowed : 11.39 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.41), residues: 493 helix: 1.45 (0.28), residues: 383 sheet: None (None), residues: 0 loop : -2.05 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 165 HIS 0.002 0.001 HIS A 226 PHE 0.013 0.002 PHE A 12 TYR 0.014 0.002 TYR A 118 ARG 0.004 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.6840 (tmt) cc_final: 0.6474 (tmm) REVERT: A 154 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 269 TYR cc_start: 0.6396 (m-10) cc_final: 0.6152 (m-10) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.1504 time to fit residues: 13.8398 Evaluate side-chains 65 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132116 restraints weight = 3389.846| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.24 r_work: 0.3542 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3867 Z= 0.267 Angle : 0.593 8.872 5272 Z= 0.300 Chirality : 0.040 0.142 634 Planarity : 0.005 0.058 639 Dihedral : 9.030 61.952 576 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.29 % Allowed : 13.16 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.41), residues: 493 helix: 1.53 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -2.03 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.001 0.001 HIS A 226 PHE 0.019 0.002 PHE A 12 TYR 0.013 0.001 TYR A 118 ARG 0.002 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.398 Fit side-chains REVERT: A 154 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8099 (tt) outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 0.1548 time to fit residues: 13.0567 Evaluate side-chains 62 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134472 restraints weight = 3306.824| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.23 r_work: 0.3509 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3867 Z= 0.220 Angle : 0.571 8.603 5272 Z= 0.287 Chirality : 0.038 0.178 634 Planarity : 0.005 0.058 639 Dihedral : 8.363 65.593 576 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.29 % Allowed : 14.18 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.41), residues: 493 helix: 1.66 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.83 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.001 0.001 HIS A 226 PHE 0.021 0.002 PHE A 12 TYR 0.009 0.001 TYR A 120 ARG 0.006 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.417 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.1466 time to fit residues: 13.3565 Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.157296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135898 restraints weight = 3345.562| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.27 r_work: 0.3529 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3867 Z= 0.193 Angle : 0.549 8.535 5272 Z= 0.273 Chirality : 0.037 0.145 634 Planarity : 0.004 0.058 639 Dihedral : 7.623 69.375 574 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.28 % Allowed : 16.20 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.41), residues: 493 helix: 1.78 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.68 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 PHE 0.020 0.002 PHE A 518 TYR 0.008 0.001 TYR A 120 ARG 0.004 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.403 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.1557 time to fit residues: 13.5706 Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 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 = 0.3877 r_free = 0.3877 target = 0.161702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141635 restraints weight = 3306.227| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.20 r_work: 0.3484 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3867 Z= 0.264 Angle : 0.586 8.435 5272 Z= 0.290 Chirality : 0.039 0.144 634 Planarity : 0.004 0.058 639 Dihedral : 7.592 70.149 574 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.04 % Allowed : 16.96 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.41), residues: 493 helix: 1.68 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.73 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 PHE 0.021 0.002 PHE A 12 TYR 0.009 0.001 TYR A 120 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.376 Fit side-chains REVERT: A 15 TRP cc_start: 0.6346 (m-90) cc_final: 0.5567 (m100) REVERT: A 268 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7188 (mpp80) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.1486 time to fit residues: 12.6308 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133488 restraints weight = 3392.421| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.26 r_work: 0.3494 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3867 Z= 0.255 Angle : 0.588 8.811 5272 Z= 0.291 Chirality : 0.038 0.144 634 Planarity : 0.005 0.057 639 Dihedral : 7.519 71.776 574 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.80 % Allowed : 16.71 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.41), residues: 493 helix: 1.64 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.64 (0.67), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 PHE 0.016 0.002 PHE A 12 TYR 0.010 0.001 TYR A 120 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.658 Fit side-chains REVERT: A 15 TRP cc_start: 0.6398 (m-90) cc_final: 0.5601 (m100) REVERT: A 268 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7219 (mpp80) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.1621 time to fit residues: 15.2852 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141732 restraints weight = 3321.748| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.20 r_work: 0.3516 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3867 Z= 0.259 Angle : 0.590 8.484 5272 Z= 0.295 Chirality : 0.039 0.167 634 Planarity : 0.005 0.058 639 Dihedral : 7.500 73.020 574 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.53 % Allowed : 18.23 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.40), residues: 493 helix: 1.66 (0.28), residues: 385 sheet: None (None), residues: 0 loop : -1.68 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.001 0.001 HIS A 273 PHE 0.014 0.002 PHE A 12 TYR 0.012 0.001 TYR A 348 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.366 Fit side-chains REVERT: A 15 TRP cc_start: 0.6390 (m-90) cc_final: 0.5590 (m100) REVERT: A 268 ARG cc_start: 0.7715 (mtt90) cc_final: 0.7226 (mpp80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.1543 time to fit residues: 12.3329 Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 0.0020 chunk 11 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.163293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143493 restraints weight = 3264.065| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.17 r_work: 0.3555 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3867 Z= 0.201 Angle : 0.555 9.027 5272 Z= 0.277 Chirality : 0.037 0.164 634 Planarity : 0.004 0.056 639 Dihedral : 7.362 75.061 574 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.53 % Allowed : 18.23 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.41), residues: 493 helix: 1.81 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.55 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 PHE 0.013 0.001 PHE A 12 TYR 0.009 0.001 TYR A 348 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.369 Fit side-chains REVERT: A 15 TRP cc_start: 0.6412 (m-90) cc_final: 0.5623 (m100) REVERT: A 268 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7267 (mpp80) outliers start: 10 outliers final: 10 residues processed: 67 average time/residue: 0.1617 time to fit residues: 13.5412 Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.0030 chunk 38 optimal weight: 0.1980 chunk 33 optimal weight: 0.3980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148080 restraints weight = 2375.828| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 0.93 r_work: 0.3579 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3867 Z= 0.178 Angle : 0.547 10.431 5272 Z= 0.271 Chirality : 0.037 0.161 634 Planarity : 0.004 0.055 639 Dihedral : 7.273 76.922 574 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.03 % Allowed : 18.99 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.41), residues: 493 helix: 1.98 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.52 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 PHE 0.012 0.001 PHE A 12 TYR 0.010 0.001 TYR A 348 ARG 0.004 0.000 ARG A 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.351 Fit side-chains REVERT: A 15 TRP cc_start: 0.6191 (m-90) cc_final: 0.5449 (m100) REVERT: A 82 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7373 (mtp85) REVERT: A 104 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 268 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7310 (mpp80) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.1838 time to fit residues: 15.2367 Evaluate side-chains 63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.0010 chunk 34 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.161179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139508 restraints weight = 3770.441| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.33 r_work: 0.3560 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3867 Z= 0.201 Angle : 0.584 14.654 5272 Z= 0.283 Chirality : 0.037 0.156 634 Planarity : 0.004 0.055 639 Dihedral : 7.281 77.303 574 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.28 % Allowed : 18.99 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.41), residues: 493 helix: 1.98 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -1.58 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 PHE 0.012 0.001 PHE A 12 TYR 0.010 0.001 TYR A 348 ARG 0.004 0.000 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.27 seconds wall clock time: 52 minutes 47.55 seconds (3167.55 seconds total)