Starting phenix.real_space_refine on Wed Mar 5 22:47:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1o_44086/03_2025/9b1o_44086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1o_44086/03_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_44086/03_2025/9b1o_44086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1o_44086/03_2025/9b1o_44086.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1o_44086/03_2025/9b1o_44086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1o_44086/03_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-5624/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: 3.96, per 1000 atoms: 1.00 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: 1.07 Conformation dependent library (CDL) restraints added in 509.3 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: 0.39 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: 1.07 Time building geometry restraints manager: 1.27 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- 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 : 0.425 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: 0.2367 time to fit residues: 18.9851 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 : 0.425 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.164719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116550 restraints weight = 4394.505| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.57 r_work: 0.3208 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4044 Z= 0.231 Angle : 0.582 7.466 5515 Z= 0.296 Chirality : 0.040 0.129 651 Planarity : 0.005 0.047 686 Dihedral : 4.302 19.312 570 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.48 % Allowed : 5.53 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.37), residues: 513 helix: 0.80 (0.26), residues: 368 sheet: None (None), residues: 0 loop : 1.35 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.003 0.001 HIS A 242 PHE 0.014 0.002 PHE A 356 TYR 0.022 0.002 TYR A 272 ARG 0.007 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 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.416 Fit side-chains REVERT: A 6 LEU cc_start: 0.7906 (mm) cc_final: 0.7665 (mt) REVERT: A 10 VAL cc_start: 0.7936 (t) cc_final: 0.7682 (p) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1500 time to fit residues: 10.3550 Evaluate side-chains 44 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 0.7980 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.164908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116734 restraints weight = 4360.265| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.58 r_work: 0.3207 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4044 Z= 0.238 Angle : 0.558 6.626 5515 Z= 0.279 Chirality : 0.040 0.124 651 Planarity : 0.005 0.043 686 Dihedral : 3.938 17.323 570 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.24 % Allowed : 7.45 % Favored : 92.31 % 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: 1.88 (0.37), residues: 513 helix: 1.38 (0.27), residues: 352 sheet: -1.99 (1.33), residues: 10 loop : 1.49 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS A 83 PHE 0.016 0.001 PHE A 358 TYR 0.020 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 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.347 Fit side-chains REVERT: A 6 LEU cc_start: 0.7855 (mm) cc_final: 0.7642 (mt) REVERT: A 10 VAL cc_start: 0.7941 (t) cc_final: 0.7694 (p) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1244 time to fit residues: 8.1842 Evaluate side-chains 46 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU 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: 3.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.167767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120637 restraints weight = 4347.854| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.58 r_work: 0.3244 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2496 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= 0.175 Angle : 0.513 6.319 5515 Z= 0.255 Chirality : 0.038 0.134 651 Planarity : 0.005 0.044 686 Dihedral : 3.679 16.580 570 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.48 % Allowed : 8.89 % Favored : 90.62 % 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: 1.99 (0.37), residues: 513 helix: 1.66 (0.27), residues: 355 sheet: -2.20 (1.35), residues: 10 loop : 0.99 (0.54), residues: 148 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 0.012 0.001 PHE A 358 TYR 0.018 0.002 TYR A 272 ARG 0.004 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 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.383 Fit side-chains REVERT: A 10 VAL cc_start: 0.7844 (t) cc_final: 0.7642 (p) REVERT: A 55 ASP cc_start: 0.8887 (m-30) cc_final: 0.8672 (m-30) REVERT: A 272 TYR cc_start: 0.6744 (p90) cc_final: 0.5436 (m-10) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.1132 time to fit residues: 8.3260 Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116855 restraints weight = 4545.748| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.60 r_work: 0.3231 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2677 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= 0.197 Angle : 0.531 9.851 5515 Z= 0.260 Chirality : 0.038 0.136 651 Planarity : 0.004 0.044 686 Dihedral : 3.581 14.127 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.44 % Allowed : 8.17 % Favored : 90.38 % 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: 1.75 (0.27), residues: 355 sheet: -2.36 (1.36), residues: 10 loop : 0.98 (0.53), 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 0.019 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 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.477 Fit side-chains REVERT: A 94 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 272 TYR cc_start: 0.6779 (p90) cc_final: 0.5419 (m-10) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.1137 time to fit residues: 8.7174 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.164301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118333 restraints weight = 4451.453| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.58 r_work: 0.3250 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2834 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= 0.177 Angle : 0.534 9.644 5515 Z= 0.257 Chirality : 0.038 0.134 651 Planarity : 0.004 0.042 686 Dihedral : 3.492 13.196 570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.96 % Allowed : 9.38 % Favored : 89.66 % 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: 2.23 (0.37), residues: 513 helix: 1.89 (0.27), residues: 355 sheet: -2.39 (1.38), residues: 10 loop : 0.96 (0.52), 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 242 PHE 0.013 0.001 PHE A 358 TYR 0.017 0.002 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 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.584 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.1060 time to fit residues: 7.7447 Evaluate side-chains 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU 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: 4.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116039 restraints weight = 4442.071| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.60 r_work: 0.3221 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2927 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= 0.218 Angle : 0.550 10.226 5515 Z= 0.266 Chirality : 0.038 0.141 651 Planarity : 0.004 0.041 686 Dihedral : 3.503 14.380 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.44 % Allowed : 10.10 % Favored : 88.46 % 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: 2.14 (0.37), residues: 513 helix: 1.83 (0.27), residues: 357 sheet: -2.75 (1.30), residues: 10 loop : 0.93 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.016 0.001 PHE A 358 TYR 0.012 0.002 TYR A 272 ARG 0.002 0.000 ARG A 281 *********************** 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 57 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.393 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.1044 time to fit residues: 8.2803 Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 379 MET 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: 9.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.163208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116809 restraints weight = 4393.413| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.58 r_work: 0.3233 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3016 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= 0.199 Angle : 0.539 10.493 5515 Z= 0.260 Chirality : 0.038 0.140 651 Planarity : 0.004 0.040 686 Dihedral : 3.467 13.847 570 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 2.26 (0.37), residues: 513 helix: 1.91 (0.27), residues: 357 sheet: -2.67 (1.31), residues: 10 loop : 0.97 (0.53), 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 0.014 0.001 PHE A 358 TYR 0.012 0.001 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 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.390 Fit side-chains REVERT: A 272 TYR cc_start: 0.7439 (p90) cc_final: 0.5546 (m-10) outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.1063 time to fit residues: 8.5038 Evaluate side-chains 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 379 MET 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: 2.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116186 restraints weight = 4450.940| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.52 r_work: 0.3230 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3071 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= 0.202 Angle : 0.540 10.847 5515 Z= 0.260 Chirality : 0.038 0.143 651 Planarity : 0.004 0.041 686 Dihedral : 3.456 13.819 570 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.68 % Allowed : 9.62 % 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: 2.31 (0.37), residues: 513 helix: 1.96 (0.27), residues: 357 sheet: -2.66 (1.30), residues: 10 loop : 0.97 (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 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 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.404 Fit side-chains REVERT: A 272 TYR cc_start: 0.7510 (p90) cc_final: 0.5635 (m-10) REVERT: A 396 LEU cc_start: 0.8478 (tp) cc_final: 0.8194 (mt) outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.1027 time to fit residues: 8.2467 Evaluate side-chains 57 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 379 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 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 = 0.3904 r_free = 0.3904 target = 0.162699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116440 restraints weight = 4452.253| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.51 r_work: 0.3234 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3111 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= 0.200 Angle : 0.544 11.172 5515 Z= 0.263 Chirality : 0.038 0.142 651 Planarity : 0.004 0.040 686 Dihedral : 3.451 13.699 570 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.68 % Allowed : 10.10 % Favored : 88.22 % 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: 2.35 (0.37), residues: 513 helix: 1.99 (0.27), residues: 357 sheet: -2.77 (1.27), residues: 10 loop : 0.99 (0.53), 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 0.014 0.001 PHE A 358 TYR 0.012 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 59 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.413 Fit side-chains REVERT: A 272 TYR cc_start: 0.7548 (p90) cc_final: 0.5695 (m-10) REVERT: A 396 LEU cc_start: 0.8524 (tp) cc_final: 0.8214 (mt) outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.1016 time to fit residues: 8.0646 Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 379 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.166130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119141 restraints weight = 4349.953| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.54 r_work: 0.3249 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3205 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= 0.187 Angle : 0.535 11.008 5515 Z= 0.258 Chirality : 0.038 0.142 651 Planarity : 0.004 0.040 686 Dihedral : 3.421 13.253 570 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.44 % Allowed : 10.58 % 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: 2.39 (0.37), residues: 513 helix: 2.01 (0.27), residues: 357 sheet: -2.86 (1.25), residues: 10 loop : 1.05 (0.54), 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 0.014 0.001 PHE A 358 TYR 0.013 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: 2684.69 seconds wall clock time: 46 minutes 37.77 seconds (2797.77 seconds total)