Starting phenix.real_space_refine on Tue Feb 11 17:12:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrv_32736/02_2025/7wrv_32736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrv_32736/02_2025/7wrv_32736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrv_32736/02_2025/7wrv_32736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrv_32736/02_2025/7wrv_32736.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrv_32736/02_2025/7wrv_32736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrv_32736/02_2025/7wrv_32736_neut.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.060 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2087 2.51 5 N 543 2.21 5 O 621 1.98 5 H 3092 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6359 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 2966 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 186} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "U" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1814 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1579 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 5.37, per 1000 atoms: 0.84 Number of scatterers: 6359 At special positions: 0 Unit cell: (80.752, 60.976, 90.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 621 8.00 N 543 7.00 C 2087 6.00 H 3092 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 290 " - pdb=" SG CYS V 355 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 684.4 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 13.3% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.704A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.105A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.859A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'V' and resid 346 through 350 Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'U' and resid 10 through 12 removed outlier: 7.093A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.163A pdb=" N ILE U 112 " --> pdb=" O SER U 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 271 through 274 removed outlier: 5.298A pdb=" N THR V 336 " --> pdb=" O ALA V 292 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N GLN V 294 " --> pdb=" O SER V 334 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER V 334 " --> pdb=" O GLN V 294 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE V 296 " --> pdb=" O SER V 332 " (cutoff:3.500A) removed outlier: 11.711A pdb=" N SER V 332 " --> pdb=" O ILE V 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 277 through 279 removed outlier: 6.729A pdb=" N TRP V 302 " --> pdb=" O LEU V 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 277 through 279 removed outlier: 3.513A pdb=" N THR V 364 " --> pdb=" O GLN V 357 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 264 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: 2.09 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3092 1.03 - 1.23: 0 1.23 - 1.42: 1483 1.42 - 1.62: 1849 1.62 - 1.81: 20 Bond restraints: 6444 Sorted by residual: bond pdb=" N GLU U 107 " pdb=" H GLU U 107 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" N GLU U 107 " pdb=" CA GLU U 107 " ideal model delta sigma weight residual 1.456 1.482 -0.027 1.44e-02 4.82e+03 3.44e+00 bond pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ASN C 331 " pdb=" H ASN C 331 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CB MET U 81 " pdb=" CG MET U 81 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 6439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11474 2.03 - 4.07: 77 4.07 - 6.10: 3 6.10 - 8.14: 1 8.14 - 10.17: 1 Bond angle restraints: 11556 Sorted by residual: angle pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " pdb=" CD GLU U 107 " ideal model delta sigma weight residual 112.60 122.77 -10.17 1.70e+00 3.46e-01 3.58e+01 angle pdb=" CA GLU U 107 " pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " ideal model delta sigma weight residual 114.10 108.35 5.75 2.00e+00 2.50e-01 8.25e+00 angle pdb=" CA GLU U 107 " pdb=" C GLU U 107 " pdb=" O GLU U 107 " ideal model delta sigma weight residual 121.49 118.50 2.99 1.16e+00 7.43e-01 6.64e+00 angle pdb=" CB MET U 81 " pdb=" CG MET U 81 " pdb=" SD MET U 81 " ideal model delta sigma weight residual 112.70 119.95 -7.25 3.00e+00 1.11e-01 5.84e+00 angle pdb=" N ILE C 410 " pdb=" CA ILE C 410 " pdb=" C ILE C 410 " ideal model delta sigma weight residual 106.21 108.78 -2.57 1.07e+00 8.73e-01 5.78e+00 ... (remaining 11551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.08: 2848 19.08 - 38.16: 187 38.16 - 57.24: 81 57.24 - 76.33: 5 76.33 - 95.41: 5 Dihedral angle restraints: 3126 sinusoidal: 1617 harmonic: 1509 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -161.72 75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS U 22 " pdb=" SG CYS U 22 " pdb=" SG CYS U 96 " pdb=" CB CYS U 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.92 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " pdb=" CD GLU U 107 " pdb=" OE1 GLU U 107 " ideal model delta sinusoidal sigma weight residual 0.00 95.41 -95.41 1 3.00e+01 1.11e-03 1.17e+01 ... (remaining 3123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 375 0.040 - 0.079: 71 0.079 - 0.119: 42 0.119 - 0.159: 8 0.159 - 0.198: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA GLU U 107 " pdb=" N GLU U 107 " pdb=" C GLU U 107 " pdb=" CB GLU U 107 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CA ILE U 52 " pdb=" N ILE U 52 " pdb=" C ILE U 52 " pdb=" CB ILE U 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE V 342 " pdb=" N ILE V 342 " pdb=" C ILE V 342 " pdb=" CB ILE V 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 494 not shown) Planarity restraints: 991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU U 107 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CD GLU U 107 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU U 107 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU U 107 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 285 " -0.135 9.50e-02 1.11e+02 4.55e-02 2.89e+00 pdb=" NE ARG V 285 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG V 285 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG V 285 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG V 285 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG V 285 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG V 285 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG V 285 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG V 285 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP U 106 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C TRP U 106 " -0.022 2.00e-02 2.50e+03 pdb=" O TRP U 106 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU U 107 " 0.007 2.00e-02 2.50e+03 ... (remaining 988 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 453 2.21 - 2.81: 12881 2.81 - 3.40: 16507 3.40 - 4.00: 22758 4.00 - 4.60: 34243 Nonbonded interactions: 86842 Sorted by model distance: nonbonded pdb=" O GLY U 26 " pdb=" HH TYR U 32 " model vdw 1.611 2.450 nonbonded pdb=" OD1 ASP C 442 " pdb=" HH TYR C 451 " model vdw 1.644 2.450 nonbonded pdb=" HG2 GLU U 10 " pdb=" HE2 LYS U 12 " model vdw 1.682 2.440 nonbonded pdb="HH22 ARG C 454 " pdb=" O SER C 469 " model vdw 1.725 2.450 nonbonded pdb=" HG1 THR C 376 " pdb=" O ALA C 435 " model vdw 1.737 2.450 ... (remaining 86837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 : 0.003 0.033 3352 Z= 0.161 Angle : 0.601 10.169 4564 Z= 0.338 Chirality : 0.044 0.198 497 Planarity : 0.004 0.061 588 Dihedral : 14.423 95.407 1165 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.58 % Allowed : 10.14 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.27 (0.41), residues: 421 helix: -2.90 (1.06), residues: 21 sheet: 1.01 (0.43), residues: 164 loop : -0.07 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 299 HIS 0.001 0.000 HIS C 519 PHE 0.007 0.001 PHE C 490 TYR 0.021 0.001 TYR V 316 ARG 0.014 0.001 ARG V 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4841 (tttt) cc_final: 0.3259 (ttpt) REVERT: V 349 ASP cc_start: 0.6610 (m-30) cc_final: 0.6350 (m-30) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 2.6507 time to fit residues: 201.5115 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN C 505 HIS U 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.160869 restraints weight = 14255.104| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.88 r_work: 0.4057 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3352 Z= 0.226 Angle : 0.556 4.349 4564 Z= 0.302 Chirality : 0.046 0.149 497 Planarity : 0.004 0.031 588 Dihedral : 4.639 16.547 467 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.32 % Allowed : 14.78 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.07 (0.41), residues: 421 helix: -3.17 (0.94), residues: 21 sheet: 0.94 (0.42), residues: 164 loop : -0.25 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.011 0.001 PHE V 340 TYR 0.013 0.002 TYR V 316 ARG 0.003 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.5017 (OUTLIER) cc_final: 0.3287 (ttpt) REVERT: U 12 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6676 (mmmm) REVERT: U 87 ARG cc_start: 0.6970 (ptt90) cc_final: 0.6753 (mtm-85) REVERT: U 112 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8167 (mp) REVERT: V 349 ASP cc_start: 0.7028 (m-30) cc_final: 0.6802 (m-30) REVERT: V 372 GLU cc_start: 0.4951 (tp30) cc_final: 0.4689 (tm-30) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 2.6199 time to fit residues: 164.2391 Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.176116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.160697 restraints weight = 14422.848| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.85 r_work: 0.4062 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3352 Z= 0.158 Angle : 0.499 3.885 4564 Z= 0.266 Chirality : 0.045 0.138 497 Planarity : 0.004 0.024 588 Dihedral : 4.481 16.906 467 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.45 % Allowed : 17.68 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.10 (0.41), residues: 421 helix: -3.62 (1.23), residues: 14 sheet: 0.81 (0.42), residues: 164 loop : -0.44 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.009 0.001 PHE C 490 TYR 0.011 0.001 TYR C 451 ARG 0.002 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.5095 (tttt) cc_final: 0.3182 (ttmt) REVERT: U 112 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8150 (mp) REVERT: V 349 ASP cc_start: 0.7037 (m-30) cc_final: 0.6800 (m-30) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 2.4703 time to fit residues: 142.4531 Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN U 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.174275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.158743 restraints weight = 14462.637| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.83 r_work: 0.4034 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3352 Z= 0.211 Angle : 0.528 3.992 4564 Z= 0.284 Chirality : 0.045 0.139 497 Planarity : 0.004 0.048 588 Dihedral : 4.671 16.903 467 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.32 % Allowed : 16.81 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.31 (0.40), residues: 421 helix: -3.63 (1.21), residues: 14 sheet: 0.83 (0.43), residues: 159 loop : -0.70 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.002 0.001 HIS C 519 PHE 0.011 0.001 PHE C 377 TYR 0.016 0.002 TYR V 316 ARG 0.009 0.001 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4947 (tttt) cc_final: 0.3069 (ttmt) REVERT: U 10 GLU cc_start: 0.7579 (tt0) cc_final: 0.7371 (tt0) REVERT: U 78 THR cc_start: 0.6905 (m) cc_final: 0.6700 (p) REVERT: U 112 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8103 (mp) REVERT: V 349 ASP cc_start: 0.7137 (m-30) cc_final: 0.6894 (m-30) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 2.1144 time to fit residues: 122.4893 Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN U 3 GLN U 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.174024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.159413 restraints weight = 14467.345| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.74 r_work: 0.4058 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3352 Z= 0.182 Angle : 0.505 4.098 4564 Z= 0.270 Chirality : 0.045 0.135 497 Planarity : 0.004 0.031 588 Dihedral : 4.587 17.378 467 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.32 % Allowed : 17.39 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.37 (0.40), residues: 421 helix: -3.55 (1.28), residues: 14 sheet: 0.72 (0.42), residues: 159 loop : -0.69 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 PHE 0.009 0.001 PHE C 490 TYR 0.012 0.001 TYR V 316 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.486 Fit side-chains REVERT: C 386 LYS cc_start: 0.4957 (tttt) cc_final: 0.3166 (ttmt) REVERT: U 10 GLU cc_start: 0.7509 (tt0) cc_final: 0.7292 (tt0) REVERT: U 112 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7992 (mp) REVERT: V 349 ASP cc_start: 0.7108 (m-30) cc_final: 0.6874 (m-30) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 2.1629 time to fit residues: 118.6660 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.174170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.159248 restraints weight = 14537.298| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.78 r_work: 0.4060 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3352 Z= 0.167 Angle : 0.495 4.091 4564 Z= 0.264 Chirality : 0.045 0.134 497 Planarity : 0.004 0.028 588 Dihedral : 4.470 17.244 467 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.61 % Allowed : 17.68 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.38 (0.40), residues: 421 helix: -3.46 (1.35), residues: 14 sheet: 0.73 (0.42), residues: 159 loop : -0.72 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.009 0.001 PHE V 340 TYR 0.011 0.001 TYR V 316 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4938 (tttt) cc_final: 0.3154 (ttmt) REVERT: U 112 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7899 (mp) REVERT: V 349 ASP cc_start: 0.7160 (m-30) cc_final: 0.6918 (m-30) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 2.1696 time to fit residues: 114.4418 Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.173833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.158697 restraints weight = 14668.185| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.79 r_work: 0.4048 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.186 Angle : 0.504 4.146 4564 Z= 0.269 Chirality : 0.045 0.135 497 Planarity : 0.004 0.025 588 Dihedral : 4.501 17.245 467 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.48 % Allowed : 16.81 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.41 (0.40), residues: 421 helix: -3.45 (1.37), residues: 14 sheet: 0.71 (0.42), residues: 159 loop : -0.74 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 299 HIS 0.001 0.001 HIS C 505 PHE 0.009 0.001 PHE V 340 TYR 0.012 0.001 TYR V 316 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.543 Fit side-chains REVERT: C 386 LYS cc_start: 0.4948 (tttt) cc_final: 0.3141 (ttmt) REVERT: U 81 MET cc_start: 0.7818 (tmm) cc_final: 0.7610 (tmm) REVERT: U 112 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7894 (mp) REVERT: V 349 ASP cc_start: 0.7191 (m-30) cc_final: 0.6935 (m-30) REVERT: V 372 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.4371 (tm-30) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 2.4351 time to fit residues: 136.0459 Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.173482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.158847 restraints weight = 14563.447| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.74 r_work: 0.4056 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.181 Angle : 0.501 4.179 4564 Z= 0.267 Chirality : 0.045 0.134 497 Planarity : 0.004 0.025 588 Dihedral : 4.467 17.015 467 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.48 % Allowed : 17.10 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.45 (0.41), residues: 421 helix: -3.51 (1.34), residues: 14 sheet: 0.69 (0.42), residues: 159 loop : -0.77 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 299 HIS 0.002 0.001 HIS C 519 PHE 0.009 0.001 PHE V 340 TYR 0.012 0.001 TYR V 316 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.522 Fit side-chains REVERT: C 386 LYS cc_start: 0.4933 (tttt) cc_final: 0.3244 (ttmt) REVERT: C 408 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6989 (ptt90) REVERT: U 81 MET cc_start: 0.7768 (tmm) cc_final: 0.7558 (tmm) REVERT: U 112 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7870 (mp) REVERT: V 349 ASP cc_start: 0.7121 (m-30) cc_final: 0.6908 (m-30) REVERT: V 372 GLU cc_start: 0.5032 (OUTLIER) cc_final: 0.4409 (tm-30) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 2.2355 time to fit residues: 124.7552 Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.171347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.155843 restraints weight = 14393.203| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.87 r_work: 0.4000 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.230 Angle : 0.530 4.283 4564 Z= 0.285 Chirality : 0.046 0.135 497 Planarity : 0.004 0.028 588 Dihedral : 4.671 17.056 467 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.48 % Allowed : 17.68 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.56 (0.41), residues: 421 helix: -3.52 (1.31), residues: 14 sheet: 0.61 (0.43), residues: 157 loop : -0.84 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP V 299 HIS 0.001 0.001 HIS C 505 PHE 0.011 0.001 PHE V 340 TYR 0.015 0.002 TYR V 316 ARG 0.003 0.001 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4943 (tttt) cc_final: 0.3280 (ttmt) REVERT: C 408 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7094 (ptt90) REVERT: U 65 GLN cc_start: 0.6647 (tp-100) cc_final: 0.6368 (tp40) REVERT: U 81 MET cc_start: 0.7870 (tmm) cc_final: 0.7615 (tmm) REVERT: U 112 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8008 (mp) REVERT: U 118 MET cc_start: 0.6871 (ttp) cc_final: 0.6648 (ttp) REVERT: V 349 ASP cc_start: 0.7349 (m-30) cc_final: 0.7137 (m-30) REVERT: V 372 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4378 (tm-30) outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 2.3322 time to fit residues: 135.1792 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.173355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.157852 restraints weight = 14396.722| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.87 r_work: 0.4028 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3352 Z= 0.155 Angle : 0.493 4.166 4564 Z= 0.262 Chirality : 0.045 0.133 497 Planarity : 0.004 0.024 588 Dihedral : 4.371 16.680 467 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.32 % Allowed : 18.55 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.55 (0.41), residues: 421 helix: -3.45 (1.10), residues: 20 sheet: 0.59 (0.43), residues: 162 loop : -0.76 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.008 0.001 PHE V 340 TYR 0.010 0.001 TYR C 451 ARG 0.003 0.000 ARG U 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.531 Fit side-chains REVERT: C 386 LYS cc_start: 0.4892 (tttt) cc_final: 0.3132 (ttmt) REVERT: C 408 ARG cc_start: 0.7339 (ttp80) cc_final: 0.7081 (ptt90) REVERT: U 81 MET cc_start: 0.7834 (tmm) cc_final: 0.7587 (tmm) REVERT: V 349 ASP cc_start: 0.7257 (m-30) cc_final: 0.6979 (m-30) REVERT: V 372 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.4328 (tm-30) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 2.4636 time to fit residues: 126.9844 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.171876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156415 restraints weight = 14723.986| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.86 r_work: 0.4011 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.198 Angle : 0.526 6.088 4564 Z= 0.279 Chirality : 0.045 0.134 497 Planarity : 0.004 0.025 588 Dihedral : 4.487 16.733 467 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.03 % Allowed : 19.42 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.55 (0.41), residues: 421 helix: -3.39 (1.14), residues: 20 sheet: 0.79 (0.44), residues: 146 loop : -0.82 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 299 HIS 0.002 0.001 HIS C 519 PHE 0.010 0.001 PHE V 340 TYR 0.014 0.001 TYR V 316 ARG 0.003 0.000 ARG U 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6581.39 seconds wall clock time: 115 minutes 56.21 seconds (6956.21 seconds total)