Starting phenix.real_space_refine on Mon Jan 13 20:29:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1o_44086/01_2025/9b1o_44086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1o_44086/01_2025/9b1o_44086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1o_44086/01_2025/9b1o_44086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1o_44086/01_2025/9b1o_44086.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1o_44086/01_2025/9b1o_44086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1o_44086/01_2025/9b1o_44086.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2570 2.51 5 N 664 2.21 5 O 681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3945 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'NAG': 1, 'VGL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.78, per 1000 atoms: 0.96 Number of scatterers: 3945 At special positions: 0 Unit cell: (56.463, 88.913, 101.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 681 8.00 N 664 7.00 C 2570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 56 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 497.1 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 83.1% alpha, 1.2% 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 3 through 11 removed outlier: 3.785A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.752A pdb=" N SER A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.838A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.784A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.627A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.657A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 222 No H-bonds generated for 'chain 'A' and resid 221 through 222' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.152A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.163A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.680A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.569A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 332 through 339 removed outlier: 4.033A pdb=" N LEU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 364 removed outlier: 4.435A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.799A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.896A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.511A pdb=" N SER A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.780A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.701A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 482 removed outlier: 4.623A pdb=" N MET A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.679A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.704A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.599A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 267 hydrogen bonds defined for protein. 762 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: 1.11 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1245 1.35 - 1.46: 953 1.46 - 1.58: 1799 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4044 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" N PHE A 3 " pdb=" CA PHE A 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.68e+00 bond pdb=" C VAL A 320 " pdb=" O VAL A 320 " ideal model delta sigma weight residual 1.236 1.255 -0.019 1.47e-02 4.63e+03 1.65e+00 bond pdb=" C TRP A 353 " pdb=" O TRP A 353 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.37e+00 ... (remaining 4039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 5154 1.37 - 2.73: 280 2.73 - 4.09: 67 4.09 - 5.46: 12 5.46 - 6.82: 2 Bond angle restraints: 5515 Sorted by residual: angle pdb=" CA TYR A 272 " pdb=" CB TYR A 272 " pdb=" CG TYR A 272 " ideal model delta sigma weight residual 113.90 120.72 -6.82 1.80e+00 3.09e-01 1.44e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 118.90 -5.00 1.80e+00 3.09e-01 7.71e+00 angle pdb=" C VAL A 264 " pdb=" CA VAL A 264 " pdb=" CB VAL A 264 " ideal model delta sigma weight residual 114.35 111.44 2.91 1.06e+00 8.90e-01 7.55e+00 angle pdb=" N PHE A 356 " pdb=" CA PHE A 356 " pdb=" CB PHE A 356 " ideal model delta sigma weight residual 109.82 113.91 -4.09 1.52e+00 4.33e-01 7.26e+00 angle pdb=" C LEU A 271 " pdb=" N TYR A 272 " pdb=" CA TYR A 272 " ideal model delta sigma weight residual 121.58 116.48 5.10 1.95e+00 2.63e-01 6.85e+00 ... (remaining 5510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 2246 16.47 - 32.94: 115 32.94 - 49.41: 22 49.41 - 65.88: 6 65.88 - 82.34: 3 Dihedral angle restraints: 2392 sinusoidal: 920 harmonic: 1472 Sorted by residual: dihedral pdb=" CA GLU A 38 " pdb=" C GLU A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LYS A 328 " pdb=" C LYS A 328 " pdb=" N GLU A 329 " pdb=" CA GLU A 329 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 397 0.032 - 0.063: 180 0.063 - 0.095: 39 0.095 - 0.127: 31 0.127 - 0.159: 4 Chirality restraints: 651 Sorted by residual: chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA VAL A 118 " pdb=" N VAL A 118 " pdb=" C VAL A 118 " pdb=" CB VAL A 118 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 648 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 354 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C PHE A 354 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE A 354 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 355 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " -0.019 2.00e-02 2.50e+03 1.30e-02 3.38e+00 pdb=" CG TYR A 272 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 265 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.022 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1687 2.92 - 3.41: 4028 3.41 - 3.91: 6454 3.91 - 4.40: 7489 4.40 - 4.90: 12247 Nonbonded interactions: 31905 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 385 " model vdw 2.424 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.487 3.040 nonbonded pdb=" N ASP A 290 " pdb=" OD1 ASP A 290 " model vdw 2.513 3.120 nonbonded pdb=" O LEU A 417 " pdb=" OG1 THR A 420 " model vdw 2.526 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.531 3.040 ... (remaining 31900 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: 0.010 Normalize map: mean=0, sd=1: 3.040 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4044 Z= 0.283 Angle : 0.764 6.825 5515 Z= 0.421 Chirality : 0.042 0.159 651 Planarity : 0.006 0.052 686 Dihedral : 11.209 82.344 1436 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.17 (0.36), residues: 513 helix: -0.34 (0.24), residues: 372 sheet: None (None), residues: 0 loop : 1.13 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 50 HIS 0.002 0.001 HIS A 47 PHE 0.023 0.002 PHE A 344 TYR 0.031 0.002 TYR A 272 ARG 0.004 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 10 VAL cc_start: 0.7776 (t) cc_final: 0.7556 (p) REVERT: A 15 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6680 (ttt180) REVERT: A 301 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8029 (ttt90) REVERT: A 343 ARG cc_start: 0.5709 (ttp80) cc_final: 0.5345 (ttm170) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2330 time to fit residues: 18.6606 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 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 488 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116760 restraints weight = 4391.101| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.59 r_work: 0.3228 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4044 Z= 0.223 Angle : 0.580 7.246 5515 Z= 0.294 Chirality : 0.040 0.129 651 Planarity : 0.005 0.048 686 Dihedral : 4.292 19.412 570 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.48 % Allowed : 5.29 % Favored : 94.23 % 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: 1.31 (0.37), residues: 513 helix: 0.83 (0.26), residues: 368 sheet: None (None), residues: 0 loop : 1.40 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.002 PHE A 356 TYR 0.021 0.002 TYR A 272 ARG 0.006 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.430 Fit side-chains REVERT: A 6 LEU cc_start: 0.7923 (mm) cc_final: 0.7692 (mt) REVERT: A 10 VAL cc_start: 0.7879 (t) cc_final: 0.7658 (p) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.1545 time to fit residues: 10.8169 Evaluate side-chains 45 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117874 restraints weight = 4387.096| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.51 r_work: 0.3258 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4044 Z= 0.165 Angle : 0.525 6.633 5515 Z= 0.261 Chirality : 0.038 0.125 651 Planarity : 0.005 0.036 686 Dihedral : 3.827 18.860 570 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.24 % Allowed : 6.97 % Favored : 92.79 % 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: 2.11 (0.37), residues: 513 helix: 1.58 (0.27), residues: 355 sheet: -1.94 (1.31), residues: 10 loop : 1.54 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.000 HIS A 242 PHE 0.013 0.001 PHE A 356 TYR 0.019 0.002 TYR A 272 ARG 0.004 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.386 Fit side-chains REVERT: A 6 LEU cc_start: 0.7899 (mm) cc_final: 0.7648 (mt) REVERT: A 10 VAL cc_start: 0.7952 (t) cc_final: 0.7729 (p) REVERT: A 272 TYR cc_start: 0.6923 (p90) cc_final: 0.5578 (m-10) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1338 time to fit residues: 9.1109 Evaluate side-chains 47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119673 restraints weight = 4346.999| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.62 r_work: 0.3230 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4044 Z= 0.197 Angle : 0.526 6.266 5515 Z= 0.261 Chirality : 0.038 0.132 651 Planarity : 0.004 0.036 686 Dihedral : 3.640 15.190 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.24 % Allowed : 8.65 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.37), residues: 513 helix: 1.72 (0.27), residues: 355 sheet: -2.23 (1.33), residues: 10 loop : 1.09 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.414 Fit side-chains REVERT: A 10 VAL cc_start: 0.7840 (t) cc_final: 0.7623 (p) REVERT: A 272 TYR cc_start: 0.6710 (p90) cc_final: 0.5384 (m-10) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.0998 time to fit residues: 7.0648 Evaluate side-chains 47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116830 restraints weight = 4551.564| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.60 r_work: 0.3207 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4044 Z= 0.201 Angle : 0.519 6.058 5515 Z= 0.257 Chirality : 0.038 0.136 651 Planarity : 0.004 0.036 686 Dihedral : 3.555 14.171 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.96 % Allowed : 8.17 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.37), residues: 513 helix: 1.72 (0.27), residues: 358 sheet: -2.37 (1.35), residues: 10 loop : 1.03 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 358 TYR 0.019 0.002 TYR A 272 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.445 Fit side-chains REVERT: A 272 TYR cc_start: 0.6843 (p90) cc_final: 0.5449 (m-10) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1016 time to fit residues: 7.7560 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118022 restraints weight = 4455.715| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.59 r_work: 0.3243 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4044 Z= 0.182 Angle : 0.537 10.240 5515 Z= 0.258 Chirality : 0.038 0.138 651 Planarity : 0.004 0.035 686 Dihedral : 3.475 13.525 570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.48 % Allowed : 9.38 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.37), residues: 513 helix: 1.84 (0.27), residues: 358 sheet: -2.35 (1.39), residues: 10 loop : 1.05 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 358 TYR 0.018 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.383 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.0984 time to fit residues: 7.1750 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110545 restraints weight = 4477.912| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.60 r_work: 0.3148 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4044 Z= 0.398 Angle : 0.640 10.181 5515 Z= 0.315 Chirality : 0.043 0.143 651 Planarity : 0.005 0.039 686 Dihedral : 3.803 17.857 570 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.44 % Allowed : 9.62 % Favored : 88.94 % 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: 1.56 (0.37), residues: 513 helix: 1.24 (0.27), residues: 364 sheet: -2.87 (1.34), residues: 10 loop : 1.13 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.005 0.001 HIS A 83 PHE 0.021 0.002 PHE A 358 TYR 0.015 0.002 TYR A 272 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.434 Fit side-chains REVERT: A 515 GLN cc_start: 0.7609 (tp40) cc_final: 0.7362 (mm110) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1193 time to fit residues: 7.9377 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116421 restraints weight = 4367.084| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.53 r_work: 0.3221 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4044 Z= 0.219 Angle : 0.555 11.026 5515 Z= 0.270 Chirality : 0.039 0.138 651 Planarity : 0.004 0.035 686 Dihedral : 3.621 15.476 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.48 % Allowed : 10.82 % Favored : 88.70 % 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: 1.98 (0.37), residues: 513 helix: 1.67 (0.27), residues: 357 sheet: -2.83 (1.32), residues: 10 loop : 0.99 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 358 TYR 0.012 0.002 TYR A 272 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.394 Fit side-chains REVERT: A 165 ASP cc_start: 0.8561 (t70) cc_final: 0.7710 (m-30) REVERT: A 272 TYR cc_start: 0.7534 (p90) cc_final: 0.5570 (m-10) REVERT: A 425 GLU cc_start: 0.7567 (tt0) cc_final: 0.7140 (tm-30) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.1009 time to fit residues: 7.1973 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118278 restraints weight = 4407.309| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.54 r_work: 0.3240 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4044 Z= 0.191 Angle : 0.548 11.666 5515 Z= 0.264 Chirality : 0.038 0.141 651 Planarity : 0.004 0.034 686 Dihedral : 3.481 14.199 570 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.96 % Allowed : 10.10 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.37), residues: 513 helix: 1.85 (0.27), residues: 358 sheet: -2.80 (1.28), residues: 10 loop : 1.01 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.014 0.001 PHE A 358 TYR 0.012 0.001 TYR A 272 ARG 0.002 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.401 Fit side-chains REVERT: A 272 TYR cc_start: 0.7513 (p90) cc_final: 0.5568 (m-10) REVERT: A 425 GLU cc_start: 0.7580 (tt0) cc_final: 0.7152 (tm-30) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.0998 time to fit residues: 7.3710 Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115529 restraints weight = 4455.609| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.50 r_work: 0.3220 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4044 Z= 0.215 Angle : 0.564 12.119 5515 Z= 0.273 Chirality : 0.038 0.145 651 Planarity : 0.004 0.035 686 Dihedral : 3.495 14.325 570 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.96 % Allowed : 11.06 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.37), residues: 513 helix: 1.88 (0.27), residues: 357 sheet: -2.88 (1.28), residues: 10 loop : 0.98 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 358 TYR 0.013 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.388 Fit side-chains REVERT: A 272 TYR cc_start: 0.7594 (p90) cc_final: 0.5620 (m-10) REVERT: A 425 GLU cc_start: 0.7539 (tt0) cc_final: 0.7142 (tm-30) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.0993 time to fit residues: 7.0332 Evaluate side-chains 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119014 restraints weight = 4348.562| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.53 r_work: 0.3232 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4044 Z= 0.191 Angle : 0.548 11.837 5515 Z= 0.264 Chirality : 0.038 0.144 651 Planarity : 0.004 0.034 686 Dihedral : 3.428 13.464 570 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.96 % Allowed : 10.34 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.37), residues: 513 helix: 1.97 (0.27), residues: 358 sheet: -2.80 (1.31), residues: 10 loop : 1.02 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 358 TYR 0.012 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.28 seconds wall clock time: 46 minutes 55.38 seconds (2815.38 seconds total)