Starting phenix.real_space_refine on Tue Mar 3 14:52:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrv_32736/03_2026/7wrv_32736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrv_32736/03_2026/7wrv_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2026/7wrv_32736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2026/7wrv_32736_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2026/7wrv_32736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2026/7wrv_32736.map" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} 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: 1.07, per 1000 atoms: 0.17 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: 0.46 Conformation dependent library (CDL) restraints added in 243.6 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: 0.23 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: 1.34 Time building geometry restraints manager: 0.63 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: 10.870 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.490 Find NCS groups from input model: 0.020 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:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.014 0.001 ARG V 285 TYR 0.021 0.001 TYR V 316 PHE 0.007 0.001 PHE C 490 TRP 0.004 0.001 TRP V 299 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3352) covalent geometry : angle 0.60144 ( 4564) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.26776 ( 12) hydrogen bonds : bond 0.25471 ( 107) hydrogen bonds : angle 10.09049 ( 264) *********************** 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 : 0.141 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: 1.1807 time to fit residues: 89.4739 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 : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.175433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159880 restraints weight = 14325.591| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.83 r_work: 0.4046 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3358 Z= 0.172 Angle : 0.576 4.417 4576 Z= 0.314 Chirality : 0.047 0.152 497 Planarity : 0.005 0.031 588 Dihedral : 4.800 17.037 467 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.61 % Allowed : 14.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.41), residues: 421 helix: -3.15 (0.94), residues: 21 sheet: 0.92 (0.42), residues: 162 loop : -0.32 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 403 TYR 0.015 0.002 TYR V 316 PHE 0.013 0.002 PHE C 377 TRP 0.008 0.002 TRP U 47 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3352) covalent geometry : angle 0.57570 ( 4564) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.72185 ( 12) hydrogen bonds : bond 0.04309 ( 107) hydrogen bonds : angle 6.98904 ( 264) *********************** 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 64 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.170 Fit side-chains REVERT: C 386 LYS cc_start: 0.5039 (OUTLIER) cc_final: 0.3353 (ttmt) REVERT: U 48 MET cc_start: 0.7409 (mtp) cc_final: 0.7195 (mtp) REVERT: U 83 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7698 (mt) REVERT: U 87 ARG cc_start: 0.6989 (ptt90) cc_final: 0.6776 (mtm-85) REVERT: U 112 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8155 (mp) REVERT: V 349 ASP cc_start: 0.7040 (m-30) cc_final: 0.6820 (m-30) REVERT: V 372 GLU cc_start: 0.4897 (tp30) cc_final: 0.4644 (tm-30) outliers start: 9 outliers final: 2 residues processed: 63 average time/residue: 1.2192 time to fit residues: 78.7312 Evaluate side-chains 55 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain U residue 83 LEU 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 8 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.172608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157275 restraints weight = 14394.276| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.83 r_work: 0.4024 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3356 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= 0.162 Angle : 0.551 4.027 4576 Z= 0.299 Chirality : 0.046 0.140 497 Planarity : 0.004 0.026 588 Dihedral : 4.955 18.016 467 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.46 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.40), residues: 421 helix: -3.62 (1.24), residues: 14 sheet: 0.78 (0.42), residues: 159 loop : -0.77 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 408 TYR 0.016 0.002 TYR V 316 PHE 0.013 0.002 PHE C 377 TRP 0.009 0.002 TRP U 47 HIS 0.001 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3352) covalent geometry : angle 0.55124 ( 4564) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.62436 ( 12) hydrogen bonds : bond 0.04108 ( 107) hydrogen bonds : angle 6.41313 ( 264) *********************** 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 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4989 (tttt) cc_final: 0.3098 (ttmt) REVERT: U 48 MET cc_start: 0.7549 (mtp) cc_final: 0.7237 (mtp) REVERT: U 83 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7679 (mt) REVERT: U 112 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8117 (mp) REVERT: V 349 ASP cc_start: 0.7161 (m-30) cc_final: 0.6900 (m-30) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 1.0782 time to fit residues: 61.9992 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 83 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 40 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.172049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.157532 restraints weight = 14701.048| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.74 r_work: 0.4038 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3589 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= 0.139 Angle : 0.530 4.052 4576 Z= 0.285 Chirality : 0.046 0.138 497 Planarity : 0.004 0.040 588 Dihedral : 4.863 18.092 467 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.61 % Allowed : 18.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.40), residues: 421 helix: -3.57 (1.27), residues: 14 sheet: 0.65 (0.42), residues: 159 loop : -0.79 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 87 TYR 0.015 0.002 TYR V 316 PHE 0.011 0.001 PHE V 340 TRP 0.008 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3352) covalent geometry : angle 0.52957 ( 4564) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.55674 ( 12) hydrogen bonds : bond 0.03543 ( 107) hydrogen bonds : angle 6.08477 ( 264) *********************** 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: 9 poor density : 48 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4999 (tttt) cc_final: 0.3413 (ttmt) REVERT: U 48 MET cc_start: 0.7571 (mtp) cc_final: 0.7206 (mtp) REVERT: U 78 THR cc_start: 0.6880 (m) cc_final: 0.6677 (p) REVERT: U 112 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7933 (mp) REVERT: V 372 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4487 (tm-30) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 1.0006 time to fit residues: 56.7617 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 : 0.166 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 481 ASN U 3 GLN U 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.173916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159390 restraints weight = 14765.826| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.76 r_work: 0.4061 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3358 Z= 0.101 Angle : 0.488 4.007 4576 Z= 0.260 Chirality : 0.045 0.133 497 Planarity : 0.004 0.030 588 Dihedral : 4.546 17.750 467 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 19.42 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.41), residues: 421 helix: -3.51 (1.33), residues: 14 sheet: 0.66 (0.42), residues: 159 loop : -0.70 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 87 TYR 0.012 0.001 TYR C 451 PHE 0.008 0.001 PHE V 340 TRP 0.006 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 3352) covalent geometry : angle 0.48834 ( 4564) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.43100 ( 12) hydrogen bonds : bond 0.03146 ( 107) hydrogen bonds : angle 5.83151 ( 264) *********************** 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 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.107 Fit side-chains REVERT: C 386 LYS cc_start: 0.4929 (tttt) cc_final: 0.3373 (ttmt) REVERT: U 48 MET cc_start: 0.7485 (mtp) cc_final: 0.7114 (mtp) REVERT: U 83 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7565 (mt) REVERT: U 112 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7866 (mp) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 1.0163 time to fit residues: 53.2743 Evaluate side-chains 45 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN V 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.170631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.156130 restraints weight = 14544.048| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.73 r_work: 0.4022 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3358 Z= 0.181 Angle : 0.568 4.288 4576 Z= 0.308 Chirality : 0.046 0.137 497 Planarity : 0.005 0.030 588 Dihedral : 5.012 17.986 467 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.06 % Allowed : 18.26 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.41), residues: 421 helix: -3.58 (1.25), residues: 14 sheet: 0.51 (0.43), residues: 157 loop : -0.89 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 87 TYR 0.019 0.002 TYR V 316 PHE 0.013 0.002 PHE V 340 TRP 0.009 0.002 TRP U 47 HIS 0.001 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3352) covalent geometry : angle 0.56715 ( 4564) SS BOND : bond 0.00231 ( 6) SS BOND : angle 0.72696 ( 12) hydrogen bonds : bond 0.03690 ( 107) hydrogen bonds : angle 5.97126 ( 264) *********************** 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 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4991 (tttt) cc_final: 0.3399 (ttmt) REVERT: U 48 MET cc_start: 0.7618 (mtp) cc_final: 0.7213 (mtp) REVERT: U 83 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7685 (mt) REVERT: U 112 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7891 (mp) REVERT: V 372 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4388 (tm-30) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 1.0257 time to fit residues: 57.0923 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 118 MET Chi-restraints excluded: chain V residue 287 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 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.171765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.157257 restraints weight = 14509.670| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.73 r_work: 0.4036 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4143 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= 0.139 Angle : 0.530 4.264 4576 Z= 0.285 Chirality : 0.046 0.133 497 Planarity : 0.004 0.027 588 Dihedral : 4.820 17.800 467 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 19.71 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.40), residues: 421 helix: -3.54 (1.28), residues: 14 sheet: 0.50 (0.43), residues: 157 loop : -0.91 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 87 TYR 0.012 0.002 TYR V 316 PHE 0.011 0.001 PHE V 340 TRP 0.008 0.001 TRP U 47 HIS 0.004 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3352) covalent geometry : angle 0.52933 ( 4564) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.59178 ( 12) hydrogen bonds : bond 0.03342 ( 107) hydrogen bonds : angle 5.87828 ( 264) *********************** 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 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4942 (tttt) cc_final: 0.3230 (ttmt) REVERT: C 408 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6984 (ptt90) REVERT: U 48 MET cc_start: 0.7551 (mtp) cc_final: 0.7223 (mtp) REVERT: U 83 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7751 (mt) REVERT: U 112 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7868 (mp) outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 1.0772 time to fit residues: 58.8327 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155740 restraints weight = 14393.870| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.84 r_work: 0.4004 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4256 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= 0.125 Angle : 0.514 4.191 4576 Z= 0.275 Chirality : 0.045 0.133 497 Planarity : 0.004 0.027 588 Dihedral : 4.670 17.582 467 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.19 % Allowed : 19.71 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.41), residues: 421 helix: -3.62 (1.22), residues: 14 sheet: 0.55 (0.43), residues: 157 loop : -0.90 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 87 TYR 0.012 0.001 TYR V 316 PHE 0.010 0.001 PHE V 340 TRP 0.007 0.001 TRP U 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3352) covalent geometry : angle 0.51406 ( 4564) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.51437 ( 12) hydrogen bonds : bond 0.03190 ( 107) hydrogen bonds : angle 5.76935 ( 264) *********************** 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 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4916 (tttt) cc_final: 0.3144 (ttmt) REVERT: C 408 ARG cc_start: 0.7323 (ttp80) cc_final: 0.7048 (ptt90) REVERT: U 48 MET cc_start: 0.7581 (mtp) cc_final: 0.7162 (mtp) REVERT: U 83 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7728 (mt) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.9809 time to fit residues: 51.6195 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.170486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.155110 restraints weight = 14474.725| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.84 r_work: 0.3997 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3358 Z= 0.141 Angle : 0.528 4.257 4576 Z= 0.284 Chirality : 0.046 0.134 497 Planarity : 0.004 0.027 588 Dihedral : 4.730 17.618 467 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.90 % Allowed : 19.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.40), residues: 421 helix: -3.53 (1.04), residues: 20 sheet: 0.65 (0.45), residues: 146 loop : -0.98 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 87 TYR 0.013 0.002 TYR V 316 PHE 0.011 0.001 PHE V 340 TRP 0.008 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3352) covalent geometry : angle 0.52808 ( 4564) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.59126 ( 12) hydrogen bonds : bond 0.03277 ( 107) hydrogen bonds : angle 5.76478 ( 264) *********************** 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 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4915 (tttt) cc_final: 0.3132 (ttmt) REVERT: C 408 ARG cc_start: 0.7340 (ttp80) cc_final: 0.7067 (ptt90) REVERT: U 48 MET cc_start: 0.7626 (mtp) cc_final: 0.7276 (mtp) REVERT: U 83 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7735 (mt) REVERT: V 372 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4379 (tm-30) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 1.0763 time to fit residues: 55.4016 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 83 LEU 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 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.168684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.153553 restraints weight = 14305.246| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.80 r_work: 0.3979 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3358 Z= 0.204 Angle : 0.590 4.441 4576 Z= 0.321 Chirality : 0.047 0.136 497 Planarity : 0.005 0.030 588 Dihedral : 5.154 17.897 467 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.19 % Allowed : 19.13 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.41), residues: 421 helix: -3.60 (1.24), residues: 14 sheet: 0.52 (0.45), residues: 147 loop : -1.07 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 87 TYR 0.020 0.002 TYR V 316 PHE 0.015 0.002 PHE V 340 TRP 0.010 0.002 TRP U 47 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 3352) covalent geometry : angle 0.58952 ( 4564) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.79145 ( 12) hydrogen bonds : bond 0.03668 ( 107) hydrogen bonds : angle 5.96699 ( 264) ********************** 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 : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.5007 (tttt) cc_final: 0.3330 (ttmt) REVERT: C 408 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7116 (ptt90) REVERT: U 48 MET cc_start: 0.7670 (mtp) cc_final: 0.7302 (mtp) REVERT: U 83 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7799 (mt) REVERT: V 372 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4332 (tm-30) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 1.1847 time to fit residues: 62.0700 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 : 0.210 ------------------------------------------------------------------------------- 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 83 LEU 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 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.170668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155603 restraints weight = 14320.870| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.82 r_work: 0.4003 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4484 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= 0.123 Angle : 0.519 4.278 4576 Z= 0.278 Chirality : 0.046 0.136 497 Planarity : 0.004 0.028 588 Dihedral : 4.730 17.731 467 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.61 % Allowed : 19.71 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.40), residues: 421 helix: -3.76 (1.14), residues: 14 sheet: 0.64 (0.45), residues: 146 loop : -1.00 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 87 TYR 0.011 0.001 TYR C 451 PHE 0.010 0.001 PHE V 340 TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3352) covalent geometry : angle 0.51925 ( 4564) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.52895 ( 12) hydrogen bonds : bond 0.03151 ( 107) hydrogen bonds : angle 5.74881 ( 264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.29 seconds wall clock time: 56 minutes 21.88 seconds (3381.88 seconds total)