Starting phenix.real_space_refine on Sun Mar 10 18:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv0_26808/03_2024/7uv0_26808_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv0_26808/03_2024/7uv0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv0_26808/03_2024/7uv0_26808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv0_26808/03_2024/7uv0_26808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv0_26808/03_2024/7uv0_26808_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv0_26808/03_2024/7uv0_26808_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3784 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3784 Unusual residues: {' NA': 2, '3PH': 1, 'IOD': 1} Classifications: {'peptide': 501, 'undetermined': 4} Link IDs: {'PTRANS': 24, 'TRANS': 476, None: 4} Not linked: pdbres="ASP A 561 " pdbres=" NA A 701 " Not linked: pdbres=" NA A 701 " pdbres=" NA A 702 " Not linked: pdbres=" NA A 702 " pdbres="IOD A 703 " Not linked: pdbres="IOD A 703 " pdbres="3PH A 704 " Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 2.45, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 1.58 Conformation dependent library (CDL) restraints added in 639.4 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... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 71.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 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 66 removed outlier: 3.647A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 86 through 103 removed outlier: 4.119A pdb=" N LEU A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 99 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 127 through 160 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 191 through 212 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 244 through 259 removed outlier: 4.197A pdb=" N THR A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 276 through 306 removed outlier: 3.545A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 339 through 369 removed outlier: 4.119A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 408 removed outlier: 3.543A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 436 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 442 through 465 removed outlier: 3.740A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 545 removed outlier: 3.581A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 729 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: 1.07 Time building geometry restraints manager: 1.71 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: 99.85 - 106.69: 121 106.69 - 113.52: 2173 113.52 - 120.36: 1534 120.36 - 127.20: 1398 127.20 - 134.03: 46 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: 196 2.72 - 3.28: 4332 3.28 - 3.84: 6825 3.84 - 4.40: 8319 4.40 - 4.96: 14083 Nonbonded interactions: 33755 Sorted by model distance: nonbonded pdb=" O PHE A 125 " pdb=" OG SER A 126 " model vdw 2.160 2.440 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 2.440 nonbonded pdb=" O GLN A 414 " pdb=" OG1 THR A 418 " model vdw 2.338 2.440 nonbonded pdb=" O THR A 115 " pdb=" NE2 GLN A 267 " model vdw 2.343 2.520 ... (remaining 33750 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: 0.960 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: 5.130 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.180 Find NCS groups from input model: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- 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= 0.334 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 fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.391 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: 0.1623 time to fit residues: 13.0356 Evaluate side-chains 57 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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: 0.4980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3867 Z= 0.214 Angle : 0.571 8.758 5272 Z= 0.283 Chirality : 0.038 0.151 634 Planarity : 0.005 0.057 639 Dihedral : 9.291 62.198 576 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.53 % Allowed : 12.15 % Favored : 85.32 % 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: 0.97 (0.41), residues: 493 helix: 1.40 (0.28), residues: 384 sheet: None (None), residues: 0 loop : -2.09 (0.66), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 226 PHE 0.013 0.002 PHE A 12 TYR 0.010 0.001 TYR A 118 ARG 0.004 0.000 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 72 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6582 (tmm) REVERT: A 154 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 269 TYR cc_start: 0.6361 (m-10) cc_final: 0.6025 (m-10) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.1310 time to fit residues: 11.7438 Evaluate side-chains 61 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 104 LEU 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 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3867 Z= 0.194 Angle : 0.543 8.347 5272 Z= 0.272 Chirality : 0.038 0.146 634 Planarity : 0.005 0.056 639 Dihedral : 8.822 63.675 576 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.29 % Allowed : 13.42 % Favored : 83.29 % 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: 1.19 (0.42), residues: 493 helix: 1.52 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.97 (0.69), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 559 HIS 0.002 0.001 HIS A 226 PHE 0.015 0.001 PHE A 12 TYR 0.010 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 73 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 269 TYR cc_start: 0.6342 (m-10) cc_final: 0.6067 (m-10) REVERT: A 420 MET cc_start: 0.8337 (tpt) cc_final: 0.8111 (tpt) outliers start: 13 outliers final: 4 residues processed: 69 average time/residue: 0.1522 time to fit residues: 13.2751 Evaluate side-chains 58 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 552 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 40 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1421 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= 0.168 Angle : 0.537 8.588 5272 Z= 0.268 Chirality : 0.037 0.145 634 Planarity : 0.005 0.056 639 Dihedral : 8.139 67.815 576 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % 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: 1.29 (0.42), residues: 493 helix: 1.63 (0.28), residues: 384 sheet: None (None), residues: 0 loop : -2.00 (0.68), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 559 HIS 0.002 0.001 HIS A 226 PHE 0.013 0.001 PHE A 304 TYR 0.009 0.001 TYR A 118 ARG 0.002 0.000 ARG A 228 *********************** 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 69 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.376 Fit side-chains REVERT: A 104 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 232 MET cc_start: 0.7903 (mmt) cc_final: 0.7659 (mmm) REVERT: A 269 TYR cc_start: 0.6324 (m-10) cc_final: 0.6068 (m-10) outliers start: 9 outliers final: 3 residues processed: 68 average time/residue: 0.1625 time to fit residues: 13.8264 Evaluate side-chains 62 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1556 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= 0.187 Angle : 0.537 8.067 5272 Z= 0.267 Chirality : 0.037 0.145 634 Planarity : 0.005 0.057 639 Dihedral : 7.651 69.327 574 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.04 % Allowed : 17.22 % Favored : 79.75 % 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 (0.42), residues: 493 helix: 1.68 (0.28), residues: 386 sheet: None (None), residues: 0 loop : -1.87 (0.69), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 559 HIS 0.001 0.000 HIS A 226 PHE 0.018 0.002 PHE A 518 TYR 0.009 0.001 TYR A 118 ARG 0.003 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 70 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7632 (mp) REVERT: A 269 TYR cc_start: 0.6241 (m-10) cc_final: 0.5986 (m-10) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.1501 time to fit residues: 13.0588 Evaluate side-chains 67 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR 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 552 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3867 Z= 0.210 Angle : 0.546 8.722 5272 Z= 0.271 Chirality : 0.037 0.143 634 Planarity : 0.005 0.057 639 Dihedral : 7.533 70.655 574 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.54 % Allowed : 17.22 % 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: 1.25 (0.41), residues: 493 helix: 1.55 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.87 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 559 HIS 0.001 0.000 HIS A 226 PHE 0.012 0.002 PHE A 518 TYR 0.010 0.001 TYR A 118 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 75 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 269 TYR cc_start: 0.6322 (m-10) cc_final: 0.6085 (m-10) REVERT: A 383 LEU cc_start: 0.8023 (mt) cc_final: 0.7379 (mt) outliers start: 14 outliers final: 11 residues processed: 70 average time/residue: 0.1429 time to fit residues: 12.8611 Evaluate side-chains 71 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 123 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 435 MET Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1691 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= 0.195 Angle : 0.562 11.878 5272 Z= 0.273 Chirality : 0.037 0.142 634 Planarity : 0.004 0.056 639 Dihedral : 7.456 71.911 574 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.80 % Allowed : 17.22 % 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: 1.33 (0.41), residues: 493 helix: 1.60 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.82 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 559 HIS 0.001 0.000 HIS A 226 PHE 0.016 0.002 PHE A 518 TYR 0.011 0.001 TYR A 118 ARG 0.002 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 fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 15 TRP cc_start: 0.6462 (m-90) cc_final: 0.5791 (m100) REVERT: A 104 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7626 (mp) REVERT: A 269 TYR cc_start: 0.6276 (m-10) cc_final: 0.6044 (m-10) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.1592 time to fit residues: 14.3755 Evaluate side-chains 67 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 435 MET Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1769 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= 0.196 Angle : 0.558 9.110 5272 Z= 0.273 Chirality : 0.037 0.142 634 Planarity : 0.005 0.056 639 Dihedral : 7.418 72.604 574 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.53 % Allowed : 17.97 % 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: 1.34 (0.41), residues: 493 helix: 1.62 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.89 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 559 HIS 0.003 0.001 HIS A 226 PHE 0.018 0.002 PHE A 12 TYR 0.011 0.001 TYR A 118 ARG 0.004 0.000 ARG A 82 *********************** 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 69 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.418 Fit side-chains REVERT: A 15 TRP cc_start: 0.6454 (m-90) cc_final: 0.5757 (m100) REVERT: A 104 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 269 TYR cc_start: 0.6292 (m-10) cc_final: 0.6061 (m-10) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.1361 time to fit residues: 12.0783 Evaluate side-chains 65 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 552 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 chunk 45 optimal weight: 0.0370 chunk 39 optimal weight: 0.5980 overall best weight: 0.3872 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1936 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= 0.169 Angle : 0.540 9.839 5272 Z= 0.265 Chirality : 0.037 0.143 634 Planarity : 0.004 0.054 639 Dihedral : 7.307 73.611 574 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.77 % Allowed : 19.24 % 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: 1.48 (0.41), residues: 493 helix: 1.74 (0.28), residues: 386 sheet: None (None), residues: 0 loop : -1.90 (0.69), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 559 HIS 0.002 0.001 HIS A 226 PHE 0.014 0.001 PHE A 12 TYR 0.010 0.001 TYR A 118 ARG 0.005 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 fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.401 Fit side-chains REVERT: A 15 TRP cc_start: 0.6430 (m-90) cc_final: 0.5677 (m100) REVERT: A 17 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: A 269 TYR cc_start: 0.6285 (m-10) cc_final: 0.6053 (m-10) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1494 time to fit residues: 13.0868 Evaluate side-chains 65 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 552 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1906 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= 0.192 Angle : 0.558 10.011 5272 Z= 0.274 Chirality : 0.038 0.141 634 Planarity : 0.005 0.054 639 Dihedral : 7.322 73.675 574 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.77 % Allowed : 19.24 % 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: 1.46 (0.41), residues: 493 helix: 1.70 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.84 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 559 HIS 0.002 0.001 HIS A 226 PHE 0.014 0.001 PHE A 12 TYR 0.011 0.001 TYR A 118 ARG 0.005 0.000 ARG A 268 ********************** 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 66 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.400 Fit side-chains REVERT: A 15 TRP cc_start: 0.6432 (m-90) cc_final: 0.5670 (m100) REVERT: A 17 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: A 269 TYR cc_start: 0.6249 (m-10) cc_final: 0.6012 (m-10) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1531 time to fit residues: 12.3791 Evaluate side-chains 66 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR 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 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.0030 chunk 34 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.158453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137691 restraints weight = 3411.178| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.26 r_work: 0.3537 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2097 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= 0.159 Angle : 0.540 10.742 5272 Z= 0.265 Chirality : 0.037 0.142 634 Planarity : 0.004 0.054 639 Dihedral : 7.239 74.661 574 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.03 % Allowed : 19.24 % 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: 1.71 (0.41), residues: 493 helix: 1.86 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.68 (0.70), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 559 HIS 0.001 0.000 HIS A 226 PHE 0.014 0.001 PHE A 12 TYR 0.010 0.001 TYR A 118 ARG 0.006 0.000 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1277.50 seconds wall clock time: 23 minutes 38.96 seconds (1418.96 seconds total)