Starting phenix.real_space_refine on Thu Jun 5 14:21:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrv_32736/06_2025/7wrv_32736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrv_32736/06_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_32736/06_2025/7wrv_32736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrv_32736/06_2025/7wrv_32736.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrv_32736/06_2025/7wrv_32736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrv_32736/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.36, per 1000 atoms: 1.31 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: 1.69 Conformation dependent library (CDL) restraints added in 882.6 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: 0.65 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: 2.56 Time building geometry restraints manager: 2.19 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: 335.620 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:25.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 387.650 ------------------------------------------------------------------------------- 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 3358 Z= 0.128 Angle : 0.601 10.169 4576 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 Details of bonding type rmsd hydrogen bonds : bond 0.25471 ( 107) hydrogen bonds : angle 10.09049 ( 264) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.26776 ( 12) covalent geometry : bond 0.00252 ( 3352) covalent geometry : angle 0.60144 ( 4564) *********************** 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 : 0.449 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: 2.4993 time to fit residues: 190.0817 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 : 0.448 ------------------------------------------------------------------------------- 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 = 0.160870 restraints weight = 14255.103| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.88 r_work: 0.4058 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- 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 3358 Z= 0.153 Angle : 0.556 4.349 4576 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 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 107) hydrogen bonds : angle 7.06471 ( 264) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.63816 ( 12) covalent geometry : bond 0.00344 ( 3352) covalent geometry : angle 0.55566 ( 4564) *********************** 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 : 0.462 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.3291 (ttpt) REVERT: U 12 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6681 (mmmm) REVERT: U 87 ARG cc_start: 0.6985 (ptt90) cc_final: 0.6772 (mtm-85) REVERT: U 112 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8147 (mp) REVERT: V 349 ASP cc_start: 0.7023 (m-30) cc_final: 0.6799 (m-30) REVERT: V 372 GLU cc_start: 0.4955 (tp30) cc_final: 0.4696 (tm-30) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 2.5797 time to fit residues: 161.7213 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 : 0.473 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.174518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158812 restraints weight = 14371.969| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.88 r_work: 0.4037 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3358 Z= 0.135 Angle : 0.530 4.000 4576 Z= 0.285 Chirality : 0.045 0.140 497 Planarity : 0.004 0.025 588 Dihedral : 4.729 17.655 467 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.32 % Allowed : 16.23 % Favored : 81.45 % 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: -0.25 (0.41), residues: 421 helix: -3.59 (1.24), residues: 14 sheet: 0.74 (0.42), residues: 164 loop : -0.58 (0.38), residues: 243 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 0.012 0.001 PHE C 377 TYR 0.014 0.002 TYR V 316 ARG 0.002 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 107) hydrogen bonds : angle 6.32037 ( 264) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.59381 ( 12) covalent geometry : bond 0.00307 ( 3352) covalent geometry : angle 0.53029 ( 4564) *********************** 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 60 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4944 (tttt) cc_final: 0.3040 (ttmt) REVERT: U 48 MET cc_start: 0.7223 (mtp) cc_final: 0.7015 (mtp) REVERT: U 87 ARG cc_start: 0.6968 (ptt90) cc_final: 0.6764 (mtm-85) REVERT: U 112 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8110 (mp) REVERT: V 349 ASP cc_start: 0.7075 (m-30) cc_final: 0.6848 (m-30) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 2.3253 time to fit residues: 141.6724 Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 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 = 0.4246 r_free = 0.4246 target = 0.172072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.157259 restraints weight = 14715.290| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.78 r_work: 0.4034 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3358 Z= 0.155 Angle : 0.544 4.087 4576 Z= 0.293 Chirality : 0.046 0.140 497 Planarity : 0.004 0.026 588 Dihedral : 4.900 17.730 467 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.61 % Allowed : 17.39 % Favored : 80.00 % 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: -0.48 (0.40), residues: 421 helix: -3.60 (1.22), residues: 14 sheet: 0.66 (0.42), residues: 159 loop : -0.78 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.012 0.002 PHE C 377 TYR 0.018 0.002 TYR V 316 ARG 0.002 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 107) hydrogen bonds : angle 6.15423 ( 264) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.62454 ( 12) covalent geometry : bond 0.00352 ( 3352) covalent geometry : angle 0.54419 ( 4564) *********************** 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 58 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4973 (tttt) cc_final: 0.3034 (ttpt) REVERT: U 48 MET cc_start: 0.7449 (mtp) cc_final: 0.7150 (mtp) REVERT: U 81 MET cc_start: 0.7853 (tmm) cc_final: 0.7638 (tmm) REVERT: U 112 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7949 (mp) REVERT: V 349 ASP cc_start: 0.7192 (m-30) cc_final: 0.6933 (m-30) REVERT: V 372 GLU cc_start: 0.5029 (OUTLIER) cc_final: 0.4437 (tm-30) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 2.2024 time to fit residues: 125.4346 Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.173040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158406 restraints weight = 14515.084| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.76 r_work: 0.4054 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3358 Z= 0.110 Angle : 0.503 4.067 4576 Z= 0.269 Chirality : 0.046 0.133 497 Planarity : 0.004 0.049 588 Dihedral : 4.617 17.374 467 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.19 % Allowed : 17.39 % 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: -0.44 (0.40), residues: 421 helix: -3.46 (1.32), residues: 14 sheet: 0.63 (0.42), residues: 159 loop : -0.71 (0.38), 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 V 340 TYR 0.011 0.001 TYR C 451 ARG 0.010 0.001 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 107) hydrogen bonds : angle 5.89099 ( 264) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.46718 ( 12) covalent geometry : bond 0.00252 ( 3352) covalent geometry : angle 0.50308 ( 4564) *********************** 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 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.473 Fit side-chains REVERT: C 386 LYS cc_start: 0.4945 (tttt) cc_final: 0.3380 (ttmt) REVERT: U 48 MET cc_start: 0.7364 (mtp) cc_final: 0.7067 (mtp) REVERT: U 81 MET cc_start: 0.7850 (tmm) cc_final: 0.7598 (tmm) REVERT: U 112 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7899 (mp) REVERT: V 349 ASP cc_start: 0.7108 (m-30) cc_final: 0.6868 (m-30) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 1.9756 time to fit residues: 112.6083 Evaluate side-chains 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 117 THR 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: 0.2980 chunk 4 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0070 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.174211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159298 restraints weight = 14584.041| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.79 r_work: 0.4059 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3358 Z= 0.100 Angle : 0.482 4.066 4576 Z= 0.257 Chirality : 0.045 0.132 497 Planarity : 0.004 0.039 588 Dihedral : 4.422 16.887 467 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.90 % Allowed : 16.81 % 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: -0.42 (0.40), residues: 421 helix: -3.33 (1.45), residues: 14 sheet: 0.69 (0.42), residues: 159 loop : -0.75 (0.38), residues: 248 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 0.008 0.001 PHE V 340 TYR 0.010 0.001 TYR C 451 ARG 0.006 0.000 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 107) hydrogen bonds : angle 5.72245 ( 264) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.43733 ( 12) covalent geometry : bond 0.00232 ( 3352) covalent geometry : angle 0.48230 ( 4564) *********************** 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 55 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.529 Fit side-chains REVERT: C 386 LYS cc_start: 0.4927 (tttt) cc_final: 0.3198 (ttmt) REVERT: U 48 MET cc_start: 0.7369 (mtp) cc_final: 0.7124 (mtp) REVERT: U 112 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7878 (mp) REVERT: V 349 ASP cc_start: 0.7172 (m-30) cc_final: 0.6910 (m-30) REVERT: V 372 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4405 (tm-30) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 2.1167 time to fit residues: 116.2129 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.172731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158022 restraints weight = 14647.199| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.75 r_work: 0.4040 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3358 Z= 0.138 Angle : 0.515 4.194 4576 Z= 0.277 Chirality : 0.045 0.134 497 Planarity : 0.004 0.036 588 Dihedral : 4.599 17.196 467 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.77 % Allowed : 17.68 % 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: -0.48 (0.41), residues: 421 helix: -3.47 (1.34), residues: 14 sheet: 0.65 (0.42), residues: 159 loop : -0.78 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 PHE 0.010 0.001 PHE V 340 TYR 0.014 0.002 TYR V 316 ARG 0.006 0.001 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 107) hydrogen bonds : angle 5.75790 ( 264) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.58196 ( 12) covalent geometry : bond 0.00317 ( 3352) covalent geometry : angle 0.51451 ( 4564) *********************** 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 58 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.599 Fit side-chains REVERT: C 386 LYS cc_start: 0.4935 (tttt) cc_final: 0.3187 (ttmt) REVERT: U 48 MET cc_start: 0.7496 (mtp) cc_final: 0.7197 (mtp) REVERT: U 112 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7900 (mp) REVERT: V 349 ASP cc_start: 0.7204 (m-30) cc_final: 0.6936 (m-30) REVERT: V 372 GLU cc_start: 0.5073 (OUTLIER) cc_final: 0.4435 (tm-30) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 2.3763 time to fit residues: 135.9205 Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 117 THR 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: 0.0870 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.172530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157157 restraints weight = 14295.812| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.85 r_work: 0.4017 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3358 Z= 0.115 Angle : 0.495 4.175 4576 Z= 0.264 Chirality : 0.045 0.132 497 Planarity : 0.004 0.032 588 Dihedral : 4.491 17.188 467 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.77 % Allowed : 18.26 % Favored : 77.97 % 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: -0.47 (0.41), residues: 421 helix: -3.43 (1.41), residues: 14 sheet: 0.67 (0.42), residues: 159 loop : -0.79 (0.38), 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 0.009 0.001 PHE V 340 TYR 0.011 0.001 TYR V 316 ARG 0.005 0.000 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 107) hydrogen bonds : angle 5.66977 ( 264) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.50484 ( 12) covalent geometry : bond 0.00265 ( 3352) covalent geometry : angle 0.49541 ( 4564) *********************** 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 58 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4890 (tttt) cc_final: 0.3088 (ttmt) REVERT: C 408 ARG cc_start: 0.7332 (ttp80) cc_final: 0.7063 (ptt90) REVERT: U 48 MET cc_start: 0.7514 (mtp) cc_final: 0.7197 (mtp) REVERT: U 83 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (mt) REVERT: V 349 ASP cc_start: 0.7263 (m-30) cc_final: 0.7041 (m-30) REVERT: V 372 GLU cc_start: 0.4984 (OUTLIER) cc_final: 0.4388 (tm-30) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 2.9629 time to fit residues: 173.7374 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 : 0.977 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 117 THR 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: 0.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.171359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.156106 restraints weight = 14416.939| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.85 r_work: 0.4007 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3358 Z= 0.132 Angle : 0.509 4.224 4576 Z= 0.272 Chirality : 0.045 0.133 497 Planarity : 0.004 0.030 588 Dihedral : 4.550 17.374 467 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.19 % Allowed : 19.42 % Favored : 77.39 % 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: -0.60 (0.41), residues: 421 helix: -3.35 (1.17), residues: 20 sheet: 0.64 (0.43), residues: 157 loop : -0.84 (0.38), residues: 244 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 0.010 0.001 PHE V 340 TYR 0.013 0.001 TYR V 316 ARG 0.005 0.000 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 107) hydrogen bonds : angle 5.68678 ( 264) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.56970 ( 12) covalent geometry : bond 0.00304 ( 3352) covalent geometry : angle 0.50853 ( 4564) *********************** 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 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4921 (tttt) cc_final: 0.3109 (ttmt) REVERT: C 408 ARG cc_start: 0.7349 (ttp80) cc_final: 0.7081 (ptt90) REVERT: U 48 MET cc_start: 0.7598 (mtp) cc_final: 0.7274 (mtp) REVERT: U 83 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7672 (mt) REVERT: V 349 ASP cc_start: 0.7265 (m-30) cc_final: 0.7043 (m-30) REVERT: V 372 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.4392 (tm-30) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 3.3497 time to fit residues: 188.0318 Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 3.360 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 117 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 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.171318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.156088 restraints weight = 14438.379| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.84 r_work: 0.4010 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3358 Z= 0.131 Angle : 0.510 4.234 4576 Z= 0.273 Chirality : 0.045 0.133 497 Planarity : 0.004 0.029 588 Dihedral : 4.550 17.351 467 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 18.84 % Favored : 77.97 % 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: -0.60 (0.41), residues: 421 helix: -3.42 (1.12), residues: 20 sheet: 0.64 (0.43), residues: 157 loop : -0.83 (0.38), residues: 244 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 0.010 0.001 PHE V 340 TYR 0.012 0.001 TYR V 316 ARG 0.004 0.000 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 107) hydrogen bonds : angle 5.67327 ( 264) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.56382 ( 12) covalent geometry : bond 0.00300 ( 3352) covalent geometry : angle 0.50939 ( 4564) ********************** 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 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4926 (tttt) cc_final: 0.3118 (ttmt) REVERT: C 408 ARG cc_start: 0.7356 (ttp80) cc_final: 0.7099 (ptt90) REVERT: U 48 MET cc_start: 0.7577 (mtp) cc_final: 0.7253 (mtp) REVERT: V 349 ASP cc_start: 0.7265 (m-30) cc_final: 0.7047 (m-30) REVERT: V 372 GLU cc_start: 0.5064 (OUTLIER) cc_final: 0.4382 (tm-30) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 2.3287 time to fit residues: 123.7813 Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 455 LEU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 117 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: 0.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.171337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.155951 restraints weight = 14671.368| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.86 r_work: 0.4009 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3358 Z= 0.130 Angle : 0.510 4.257 4576 Z= 0.273 Chirality : 0.045 0.133 497 Planarity : 0.004 0.029 588 Dihedral : 4.551 17.427 467 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.90 % Allowed : 18.55 % 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: -0.62 (0.41), residues: 421 helix: -3.42 (1.12), residues: 20 sheet: 0.61 (0.43), residues: 157 loop : -0.85 (0.38), residues: 244 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 0.010 0.001 PHE V 340 TYR 0.011 0.001 TYR V 316 ARG 0.004 0.000 ARG U 87 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 107) hydrogen bonds : angle 5.65350 ( 264) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.55082 ( 12) covalent geometry : bond 0.00300 ( 3352) covalent geometry : angle 0.51018 ( 4564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7848.42 seconds wall clock time: 139 minutes 32.22 seconds (8372.22 seconds total)