Starting phenix.real_space_refine on Fri Dec 27 11:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7y_33674/12_2024/7y7y_33674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7y_33674/12_2024/7y7y_33674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/12_2024/7y7y_33674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7y_33674/12_2024/7y7y_33674.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7y_33674/12_2024/7y7y_33674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7y_33674/12_2024/7y7y_33674.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.109 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2838 2.51 5 N 650 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4195 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 108 Unusual residues: {' CL': 1, ' NA': 2, 'ID7': 1, 'NAG': 3} Classifications: {'undetermined': 7, 'water': 54} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.31, per 1000 atoms: 0.77 Number of scatterers: 4303 At special positions: 0 Unit cell: (69.28, 71.445, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 778 8.00 N 650 7.00 C 2838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.05 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 522.1 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.705A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.690A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.985A pdb=" N VAL A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.950A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 4.136A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.619A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.886A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 315 through 350 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.693A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.162A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.937A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.647A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.402A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 571 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 287 hydrogen bonds defined for protein. 840 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: 1.64 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 622 1.31 - 1.44: 1351 1.44 - 1.56: 2354 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4381 Sorted by residual: bond pdb=" C SER A 456 " pdb=" O SER A 456 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" CA SER A 456 " pdb=" CB SER A 456 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.21e+01 bond pdb=" C1 ID7 A 701 " pdb=" O1 ID7 A 701 " ideal model delta sigma weight residual 1.249 1.198 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 ID7 A 701 " pdb=" O2 ID7 A 701 " ideal model delta sigma weight residual 1.248 1.202 0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 ... (remaining 4376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 5856 2.18 - 4.37: 95 4.37 - 6.55: 14 6.55 - 8.73: 2 8.73 - 10.92: 1 Bond angle restraints: 5968 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.22 -10.92 2.00e+00 2.50e-01 2.98e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.74 -8.24 1.70e+00 3.46e-01 2.35e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.56 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CA ASP A 165 " pdb=" CB ASP A 165 " pdb=" CG ASP A 165 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ALA A 455 " pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 116.22 121.73 -5.51 1.44e+00 4.82e-01 1.46e+01 ... (remaining 5963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2146 17.05 - 34.11: 272 34.11 - 51.16: 75 51.16 - 68.22: 19 68.22 - 85.27: 6 Dihedral angle restraints: 2518 sinusoidal: 999 harmonic: 1519 Sorted by residual: dihedral pdb=" CA PHE A 502 " pdb=" C PHE A 502 " pdb=" N PHE A 503 " pdb=" CA PHE A 503 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -54.23 -31.77 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 662 0.274 - 0.548: 3 0.548 - 0.821: 0 0.821 - 1.095: 0 1.095 - 1.369: 1 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 663 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.008 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" CG ASN A 184 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.191 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.405 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.073 2.00e-02 2.50e+03 7.26e-02 6.60e+01 pdb=" CG ASN A 176 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.116 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.046 2.00e-02 2.50e+03 5.43e-02 3.69e+01 pdb=" CG ASN A 181 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.062 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 31 2.41 - 3.03: 2786 3.03 - 3.66: 6773 3.66 - 4.28: 10892 4.28 - 4.90: 17201 Nonbonded interactions: 37683 Sorted by model distance: nonbonded pdb=" O HOH A 803 " pdb=" O HOH A 822 " model vdw 1.789 3.040 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 805 " model vdw 1.910 3.040 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASP A 287 " pdb=" O HOH A 802 " model vdw 1.987 3.040 nonbonded pdb=" O ALA A 357 " pdb=" O HOH A 803 " model vdw 2.014 3.040 ... (remaining 37678 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 0.059 4381 Z= 0.351 Angle : 0.725 10.915 5968 Z= 0.402 Chirality : 0.072 1.369 666 Planarity : 0.005 0.034 722 Dihedral : 16.872 85.271 1551 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 26.56 % Favored : 72.99 % 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: 0.29 (0.36), residues: 525 helix: 0.73 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.11 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 161 HIS 0.005 0.002 HIS A 198 PHE 0.027 0.003 PHE A 398 TYR 0.027 0.002 TYR A 72 ARG 0.004 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.481 Fit side-chains REVERT: A 572 GLN cc_start: 0.7403 (tp40) cc_final: 0.7069 (tt0) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 1.3350 time to fit residues: 89.9558 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 487 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS A 483 ASN A 534 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4381 Z= 0.237 Angle : 0.602 7.645 5968 Z= 0.320 Chirality : 0.044 0.235 666 Planarity : 0.004 0.034 722 Dihedral : 5.552 50.696 650 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 22.77 % Favored : 74.33 % 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: 0.98 (0.37), residues: 525 helix: 1.26 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.530 Fit side-chains REVERT: A 163 GLN cc_start: 0.8158 (mt0) cc_final: 0.7949 (mt0) REVERT: A 485 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 559 LEU cc_start: 0.7896 (mt) cc_final: 0.7670 (mt) REVERT: A 572 GLN cc_start: 0.7318 (tp40) cc_final: 0.6978 (tt0) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 1.1642 time to fit residues: 84.8154 Evaluate side-chains 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4381 Z= 0.206 Angle : 0.566 7.603 5968 Z= 0.296 Chirality : 0.043 0.213 666 Planarity : 0.004 0.033 722 Dihedral : 5.199 52.184 647 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 22.77 % Favored : 74.55 % 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: 1.27 (0.37), residues: 525 helix: 1.51 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.10 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.021 0.002 TYR A 72 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.489 Fit side-chains REVERT: A 179 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5960 (mpm) REVERT: A 348 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8366 (t) REVERT: A 559 LEU cc_start: 0.7945 (mt) cc_final: 0.7636 (mt) REVERT: A 572 GLN cc_start: 0.7300 (tp40) cc_final: 0.6972 (tt0) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 1.0586 time to fit residues: 79.5831 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4381 Z= 0.218 Angle : 0.577 8.875 5968 Z= 0.301 Chirality : 0.043 0.195 666 Planarity : 0.004 0.034 722 Dihedral : 5.106 53.110 647 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.12 % Allowed : 21.43 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.37), residues: 525 helix: 1.56 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.06 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.523 Fit side-chains REVERT: A 348 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (t) REVERT: A 485 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 487 MET cc_start: 0.8368 (mtm) cc_final: 0.8159 (mtm) REVERT: A 559 LEU cc_start: 0.7924 (mt) cc_final: 0.7579 (mt) REVERT: A 572 GLN cc_start: 0.7309 (tp40) cc_final: 0.6969 (tt0) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 1.0995 time to fit residues: 82.6415 Evaluate side-chains 72 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4381 Z= 0.211 Angle : 0.567 8.711 5968 Z= 0.295 Chirality : 0.043 0.191 666 Planarity : 0.004 0.034 722 Dihedral : 4.999 53.469 647 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.12 % Allowed : 20.54 % Favored : 76.34 % 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: 1.38 (0.37), residues: 525 helix: 1.58 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.08 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.022 0.002 TYR A 72 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.502 Fit side-chains REVERT: A 348 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8361 (t) REVERT: A 485 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: A 559 LEU cc_start: 0.8060 (mt) cc_final: 0.7703 (mt) REVERT: A 572 GLN cc_start: 0.7317 (tp40) cc_final: 0.6975 (tt0) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 1.2171 time to fit residues: 88.6130 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.0060 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4381 Z= 0.231 Angle : 0.588 9.973 5968 Z= 0.305 Chirality : 0.044 0.184 666 Planarity : 0.004 0.035 722 Dihedral : 4.977 53.604 647 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.35 % Allowed : 19.87 % Favored : 76.79 % 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 (0.37), residues: 525 helix: 1.56 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.09 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.442 Fit side-chains REVERT: A 348 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8365 (t) REVERT: A 485 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: A 559 LEU cc_start: 0.8056 (mt) cc_final: 0.7697 (mt) REVERT: A 572 GLN cc_start: 0.7325 (tp40) cc_final: 0.6981 (tt0) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 1.1783 time to fit residues: 87.0879 Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4381 Z= 0.218 Angle : 0.582 10.285 5968 Z= 0.300 Chirality : 0.043 0.181 666 Planarity : 0.004 0.033 722 Dihedral : 4.906 54.015 647 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.12 % Allowed : 19.87 % Favored : 77.01 % 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: 1.38 (0.37), residues: 525 helix: 1.58 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.04 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.005 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.512 Fit side-chains REVERT: A 179 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5970 (mpm) REVERT: A 348 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8338 (t) REVERT: A 485 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: A 559 LEU cc_start: 0.8053 (mt) cc_final: 0.7709 (mt) REVERT: A 572 GLN cc_start: 0.7330 (tp40) cc_final: 0.6983 (tt0) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 1.2987 time to fit residues: 109.0393 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4381 Z= 0.247 Angle : 0.610 10.861 5968 Z= 0.315 Chirality : 0.044 0.180 666 Planarity : 0.004 0.034 722 Dihedral : 4.947 53.824 647 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 20.54 % Favored : 76.56 % 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 (0.37), residues: 525 helix: 1.56 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.07 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.024 0.002 TYR A 72 ARG 0.007 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.477 Fit side-chains REVERT: A 179 MET cc_start: 0.6143 (mpm) cc_final: 0.5822 (mpm) REVERT: A 485 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 559 LEU cc_start: 0.8038 (mt) cc_final: 0.7724 (mt) REVERT: A 572 GLN cc_start: 0.7329 (tp40) cc_final: 0.6982 (tt0) outliers start: 13 outliers final: 12 residues processed: 74 average time/residue: 1.2599 time to fit residues: 97.1134 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 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 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4381 Z= 0.209 Angle : 0.583 11.609 5968 Z= 0.299 Chirality : 0.042 0.176 666 Planarity : 0.004 0.034 722 Dihedral : 4.824 54.259 647 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 20.31 % Favored : 76.79 % 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: 1.44 (0.37), residues: 525 helix: 1.58 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.90 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.022 0.002 TYR A 72 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.490 Fit side-chains REVERT: A 57 CYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8333 (m) REVERT: A 179 MET cc_start: 0.5966 (mpm) cc_final: 0.5619 (mpm) REVERT: A 348 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8304 (t) REVERT: A 485 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: A 559 LEU cc_start: 0.8031 (mt) cc_final: 0.7661 (mt) REVERT: A 572 GLN cc_start: 0.7332 (tp40) cc_final: 0.6984 (tt0) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 1.3434 time to fit residues: 110.0680 Evaluate side-chains 77 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4381 Z= 0.200 Angle : 0.580 11.897 5968 Z= 0.296 Chirality : 0.042 0.175 666 Planarity : 0.004 0.033 722 Dihedral : 4.744 54.266 647 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.12 % Allowed : 19.87 % Favored : 77.01 % 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: 1.49 (0.37), residues: 525 helix: 1.61 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.88 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.022 0.001 TYR A 72 ARG 0.006 0.001 ARG A 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.479 Fit side-chains REVERT: A 179 MET cc_start: 0.6038 (OUTLIER) cc_final: 0.5746 (mpm) REVERT: A 348 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8295 (t) REVERT: A 485 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 559 LEU cc_start: 0.8002 (mt) cc_final: 0.7629 (mt) REVERT: A 572 GLN cc_start: 0.7402 (tp40) cc_final: 0.7060 (tt0) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 1.2400 time to fit residues: 100.2661 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 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 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.092662 restraints weight = 4230.708| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.34 r_work: 0.2824 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4381 Z= 0.222 Angle : 0.588 9.812 5968 Z= 0.304 Chirality : 0.043 0.183 666 Planarity : 0.004 0.033 722 Dihedral : 4.790 54.233 647 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 19.87 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.37), residues: 525 helix: 1.60 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.93 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.007 0.001 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.63 seconds wall clock time: 37 minutes 23.60 seconds (2243.60 seconds total)