Starting phenix.real_space_refine on Tue Aug 4 14:45:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vh9_65060/08_2026/9vh9_65060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vh9_65060/08_2026/9vh9_65060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vh9_65060/08_2026/9vh9_65060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vh9_65060/08_2026/9vh9_65060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vh9_65060/08_2026/9vh9_65060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vh9_65060/08_2026/9vh9_65060.map" } resolution = 3.4 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 2623 2.51 5 N 636 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3971 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 3932 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ARG:plan': 12, 'HIS:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 160 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'P2E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.75, per 1000 atoms: 0.19 Number of scatterers: 3971 At special positions: 0 Unit cell: (79.22, 88.54, 75.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 680 8.00 N 636 7.00 C 2623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 594 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 491 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 152.0 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 71.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 3.678A pdb=" N ASN A 30 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 63 removed outlier: 4.923A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 91 removed outlier: 3.587A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.748A pdb=" N LEU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.557A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 203 through 229 removed outlier: 3.817A pdb=" N PHE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.724A pdb=" N MET A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.594A pdb=" N ARG A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 314' Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 325 through 348 removed outlier: 3.716A pdb=" N VAL A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 360 through 390 removed outlier: 4.759A pdb=" N LEU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 396 through 413 Processing helix chain 'A' and resid 413 through 419 removed outlier: 4.331A pdb=" N PHE A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 514 through 531 Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.542A pdb=" N MET A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 566 through 579 removed outlier: 3.833A pdb=" N ALA A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 459 Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 489 272 hydrogen bonds defined for protein. 801 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: 0.37 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 601 1.32 - 1.44: 1147 1.44 - 1.57: 2279 1.57 - 1.70: 2 1.70 - 1.83: 44 Bond restraints: 4073 Sorted by residual: bond pdb=" C10 P2E A 702 " pdb=" C9 P2E A 702 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C11 P2E A 702 " pdb=" C12 P2E A 702 " ideal model delta sigma weight residual 1.529 1.428 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C10 P2E A 702 " pdb=" C11 P2E A 702 " ideal model delta sigma weight residual 1.529 1.605 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C6 P2E A 702 " pdb=" C7 P2E A 702 " ideal model delta sigma weight residual 1.499 1.556 -0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C7 P2E A 702 " pdb=" C8 P2E A 702 " ideal model delta sigma weight residual 1.529 1.475 0.054 2.00e-02 2.50e+03 7.41e+00 ... (remaining 4068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 5514 3.26 - 6.52: 44 6.52 - 9.78: 4 9.78 - 13.04: 3 13.04 - 16.30: 1 Bond angle restraints: 5566 Sorted by residual: angle pdb=" C5 P2E A 702 " pdb=" C6 P2E A 702 " pdb=" C7 P2E A 702 " ideal model delta sigma weight residual 125.83 109.53 16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" C12 P2E A 702 " pdb=" C13 P2E A 702 " pdb=" C14 P2E A 702 " ideal model delta sigma weight residual 124.37 111.43 12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C4 P2E A 702 " pdb=" C5 P2E A 702 " pdb=" C6 P2E A 702 " ideal model delta sigma weight residual 127.52 115.06 12.46 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C13 P2E A 702 " pdb=" C14 P2E A 702 " pdb=" C15 P2E A 702 " ideal model delta sigma weight residual 125.85 115.09 10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C ILE A 477 " pdb=" CA ILE A 477 " pdb=" CB ILE A 477 " ideal model delta sigma weight residual 111.59 108.38 3.21 1.10e+00 8.26e-01 8.52e+00 ... (remaining 5561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.59: 2086 12.59 - 25.18: 206 25.18 - 37.78: 65 37.78 - 50.37: 25 50.37 - 62.96: 8 Dihedral angle restraints: 2390 sinusoidal: 795 harmonic: 1595 Sorted by residual: dihedral pdb=" CB CYS A 450 " pdb=" SG CYS A 450 " pdb=" SG CYS A 470 " pdb=" CB CYS A 470 " ideal model delta sinusoidal sigma weight residual 93.00 30.04 62.96 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 48.50 44.50 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 492 " pdb=" CB CYS A 492 " ideal model delta sinusoidal sigma weight residual 93.00 60.16 32.84 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 2387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 610 0.084 - 0.169: 49 0.169 - 0.253: 1 0.253 - 0.337: 1 0.337 - 0.421: 2 Chirality restraints: 663 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 491 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C8 P2E A 702 " pdb=" C12 P2E A 702 " pdb=" C7 P2E A 702 " pdb=" C9 P2E A 702 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C15 P2E A 702 " pdb=" C14 P2E A 702 " pdb=" C16 P2E A 702 " pdb=" O5 P2E A 702 " both_signs ideal model delta sigma weight residual False 2.23 2.50 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 660 not shown) Planarity restraints: 699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.083 2.00e-02 2.50e+03 6.83e-02 5.84e+01 pdb=" C7 NAG A 701 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.108 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 534 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO A 535 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 566 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 567 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 567 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 567 " -0.022 5.00e-02 4.00e+02 ... (remaining 696 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 706 2.76 - 3.29: 4155 3.29 - 3.83: 6734 3.83 - 4.36: 7098 4.36 - 4.90: 12500 Nonbonded interactions: 31193 Sorted by model distance: nonbonded pdb=" O GLY A 344 " pdb=" OH TYR A 606 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLN A 335 " pdb=" NE2 GLN A 556 " model vdw 2.238 3.120 nonbonded pdb=" OH TYR A 90 " pdb=" O PHE A 311 " model vdw 2.392 3.040 nonbonded pdb=" O LYS A 355 " pdb=" ND2 ASN A 599 " model vdw 2.416 3.120 nonbonded pdb=" NH1 ARG A 97 " pdb=" OG SER A 193 " model vdw 2.425 3.120 ... (remaining 31188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.820 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.005 0.122 4080 Z= 0.237 Angle : 0.828 16.298 5581 Z= 0.397 Chirality : 0.050 0.421 663 Planarity : 0.006 0.068 698 Dihedral : 12.549 61.323 1346 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.37), residues: 547 helix: 1.94 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.66 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 582 TYR 0.016 0.001 TYR A 48 PHE 0.019 0.001 PHE A 366 TRP 0.003 0.001 TRP A 565 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.24 ( 4073) covalent geometry : angle 0.81205 / 0.39 ( 5566) SS BOND : bond 0.00471 / 0.28 ( 6) SS BOND : angle 1.81557 / 1.03 ( 12) hydrogen bonds : bond 0.13400 / 8.42 ( 272) hydrogen bonds : angle 5.55689 / 3.92 ( 801) link_NAG-ASN : bond 0.01996 / 1.05 ( 1) link_NAG-ASN : angle 6.33739 / 3.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.149 Fit side-chains REVERT: A 106 LEU cc_start: 0.8755 (mm) cc_final: 0.8468 (mm) REVERT: A 257 TRP cc_start: 0.7049 (p-90) cc_final: 0.6597 (p-90) REVERT: A 546 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 599 ASN cc_start: 0.6806 (m110) cc_final: 0.6297 (m110) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0652 time to fit residues: 9.8870 Evaluate side-chains 101 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.183963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144237 restraints weight = 6359.594| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 4.11 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4080 Z= 0.142 Angle : 0.644 9.123 5581 Z= 0.310 Chirality : 0.043 0.196 663 Planarity : 0.005 0.046 698 Dihedral : 6.035 56.498 631 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 1.38 % Allowed : 12.40 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.61 (0.37), residues: 547 helix: 1.89 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.46 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.014 0.002 TYR A 51 PHE 0.023 0.002 PHE A 557 TRP 0.006 0.001 TRP A 583 HIS 0.001 0.000 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4073) covalent geometry : angle 0.64171 / 0.31 ( 5566) SS BOND : bond 0.00262 / 0.17 ( 6) SS BOND : angle 1.00780 / 0.57 ( 12) hydrogen bonds : bond 0.04048 / 2.68 ( 272) hydrogen bonds : angle 4.55492 / 3.24 ( 801) link_NAG-ASN : bond 0.00183 / 0.10 ( 1) link_NAG-ASN : angle 1.80405 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8818 (mm) cc_final: 0.8429 (mm) REVERT: A 229 MET cc_start: 0.8143 (ptp) cc_final: 0.7850 (ptp) REVERT: A 311 PHE cc_start: 0.7283 (t80) cc_final: 0.6567 (m-80) REVERT: A 387 MET cc_start: 0.7076 (mmm) cc_final: 0.6792 (mmt) REVERT: A 456 HIS cc_start: 0.6890 (m170) cc_final: 0.6586 (m170) REVERT: A 599 ASN cc_start: 0.6834 (m110) cc_final: 0.6030 (m110) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.0510 time to fit residues: 6.6159 Evaluate side-chains 102 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 525 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 188 GLN A 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.188091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147021 restraints weight = 6345.892| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 4.22 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4080 Z= 0.120 Angle : 0.626 11.392 5581 Z= 0.297 Chirality : 0.042 0.185 663 Planarity : 0.005 0.045 698 Dihedral : 5.616 53.346 631 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 1.10 % Allowed : 16.80 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.37), residues: 547 helix: 1.82 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.41 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.011 0.001 TYR A 357 PHE 0.018 0.001 PHE A 557 TRP 0.005 0.001 TRP A 583 HIS 0.000 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4073) covalent geometry : angle 0.62426 / 0.30 ( 5566) SS BOND : bond 0.00237 / 0.16 ( 6) SS BOND : angle 0.79722 / 0.45 ( 12) hydrogen bonds : bond 0.03789 / 2.52 ( 272) hydrogen bonds : angle 4.37223 / 3.09 ( 801) link_NAG-ASN : bond 0.00431 / 0.23 ( 1) link_NAG-ASN : angle 1.55144 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8617 (tpm170) cc_final: 0.8396 (tpm170) REVERT: A 106 LEU cc_start: 0.8778 (mm) cc_final: 0.8292 (mm) REVERT: A 311 PHE cc_start: 0.7528 (t80) cc_final: 0.6808 (m-80) REVERT: A 387 MET cc_start: 0.7099 (mmm) cc_final: 0.6596 (mmm) REVERT: A 409 MET cc_start: 0.7941 (mtt) cc_final: 0.7553 (mtt) REVERT: A 456 HIS cc_start: 0.6842 (m170) cc_final: 0.6552 (m170) REVERT: A 582 ARG cc_start: 0.7075 (mtp-110) cc_final: 0.6762 (mmm160) REVERT: A 599 ASN cc_start: 0.6491 (m110) cc_final: 0.5882 (m110) outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.0620 time to fit residues: 8.0153 Evaluate side-chains 100 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 187 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.182010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140246 restraints weight = 6276.359| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 4.17 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4080 Z= 0.150 Angle : 0.642 8.699 5581 Z= 0.308 Chirality : 0.043 0.177 663 Planarity : 0.004 0.044 698 Dihedral : 5.438 50.981 631 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.53 % Rotamer: Outliers : 1.65 % Allowed : 19.83 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.37), residues: 547 helix: 1.76 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.40 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.015 0.002 TYR A 207 PHE 0.014 0.002 PHE A 34 TRP 0.007 0.001 TRP A 583 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4073) covalent geometry : angle 0.64132 / 0.31 ( 5566) SS BOND : bond 0.00202 / 0.12 ( 6) SS BOND : angle 0.74054 / 0.41 ( 12) hydrogen bonds : bond 0.03889 / 2.64 ( 272) hydrogen bonds : angle 4.38275 / 3.09 ( 801) link_NAG-ASN : bond 0.00405 / 0.21 ( 1) link_NAG-ASN : angle 1.33619 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8750 (tpm170) cc_final: 0.8470 (tpm170) REVERT: A 106 LEU cc_start: 0.8910 (mm) cc_final: 0.8341 (mm) REVERT: A 229 MET cc_start: 0.8037 (ptp) cc_final: 0.7692 (ptp) REVERT: A 257 TRP cc_start: 0.7138 (p-90) cc_final: 0.6295 (p-90) REVERT: A 311 PHE cc_start: 0.7456 (t80) cc_final: 0.6820 (m-80) REVERT: A 387 MET cc_start: 0.7188 (mmm) cc_final: 0.6729 (mmm) REVERT: A 389 ARG cc_start: 0.7877 (mmt-90) cc_final: 0.7599 (mmt-90) REVERT: A 409 MET cc_start: 0.7972 (mtt) cc_final: 0.7635 (mtt) REVERT: A 582 ARG cc_start: 0.7124 (mtp-110) cc_final: 0.6828 (mmm160) REVERT: A 599 ASN cc_start: 0.6445 (m110) cc_final: 0.5691 (m110) REVERT: A 606 TYR cc_start: 0.8124 (t80) cc_final: 0.7888 (t80) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.0608 time to fit residues: 7.5430 Evaluate side-chains 95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 607 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.182250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141068 restraints weight = 6226.096| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.14 r_work: 0.3735 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4080 Z= 0.141 Angle : 0.650 12.128 5581 Z= 0.308 Chirality : 0.043 0.173 663 Planarity : 0.004 0.044 698 Dihedral : 5.352 52.038 631 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 1.65 % Allowed : 22.04 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.37), residues: 547 helix: 1.74 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.40 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 561 TYR 0.014 0.002 TYR A 357 PHE 0.015 0.001 PHE A 34 TRP 0.005 0.001 TRP A 583 HIS 0.001 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4073) covalent geometry : angle 0.64941 / 0.31 ( 5566) SS BOND : bond 0.00198 / 0.11 ( 6) SS BOND : angle 0.64816 / 0.36 ( 12) hydrogen bonds : bond 0.03874 / 2.68 ( 272) hydrogen bonds : angle 4.35183 / 3.04 ( 801) link_NAG-ASN : bond 0.00416 / 0.22 ( 1) link_NAG-ASN : angle 1.28059 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8702 (tpm170) cc_final: 0.8484 (tpm170) REVERT: A 106 LEU cc_start: 0.8940 (mm) cc_final: 0.8383 (mm) REVERT: A 257 TRP cc_start: 0.7176 (p-90) cc_final: 0.6156 (p-90) REVERT: A 311 PHE cc_start: 0.7657 (t80) cc_final: 0.6907 (m-80) REVERT: A 368 ILE cc_start: 0.8606 (mm) cc_final: 0.8367 (mt) REVERT: A 409 MET cc_start: 0.8172 (mtt) cc_final: 0.7826 (mtt) REVERT: A 582 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.7000 (mmm160) REVERT: A 599 ASN cc_start: 0.6451 (m110) cc_final: 0.5835 (m110) outliers start: 6 outliers final: 3 residues processed: 101 average time/residue: 0.0665 time to fit residues: 8.4823 Evaluate side-chains 97 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 607 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.185615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.142839 restraints weight = 6333.561| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 4.26 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4080 Z= 0.128 Angle : 0.657 11.845 5581 Z= 0.309 Chirality : 0.042 0.168 663 Planarity : 0.004 0.041 698 Dihedral : 5.239 54.304 631 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 2.48 % Allowed : 23.42 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.36), residues: 547 helix: 1.69 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.36 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 97 TYR 0.011 0.001 TYR A 357 PHE 0.013 0.001 PHE A 34 TRP 0.005 0.001 TRP A 583 HIS 0.001 0.000 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4073) covalent geometry : angle 0.65582 / 0.31 ( 5566) SS BOND : bond 0.00157 / 0.11 ( 6) SS BOND : angle 0.89524 / 0.49 ( 12) hydrogen bonds : bond 0.03780 / 2.58 ( 272) hydrogen bonds : angle 4.27253 / 2.97 ( 801) link_NAG-ASN : bond 0.00420 / 0.22 ( 1) link_NAG-ASN : angle 1.22368 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8194 (tt) REVERT: A 62 ARG cc_start: 0.8751 (tpm170) cc_final: 0.8544 (tpm170) REVERT: A 106 LEU cc_start: 0.8926 (mm) cc_final: 0.8283 (mm) REVERT: A 229 MET cc_start: 0.8006 (ptp) cc_final: 0.7695 (ptp) REVERT: A 257 TRP cc_start: 0.7162 (p-90) cc_final: 0.6383 (p-90) REVERT: A 311 PHE cc_start: 0.7546 (t80) cc_final: 0.6860 (m-80) REVERT: A 351 LYS cc_start: 0.6232 (mtpt) cc_final: 0.5938 (ttpt) REVERT: A 387 MET cc_start: 0.7120 (mmp) cc_final: 0.6891 (mmt) REVERT: A 409 MET cc_start: 0.7931 (mtt) cc_final: 0.7614 (mtt) REVERT: A 582 ARG cc_start: 0.6946 (mtp-110) cc_final: 0.6711 (mmm160) REVERT: A 599 ASN cc_start: 0.6493 (m110) cc_final: 0.5691 (m110) outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.0657 time to fit residues: 8.7157 Evaluate side-chains 101 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 607 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.182898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.141200 restraints weight = 6446.377| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 4.23 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4080 Z= 0.141 Angle : 0.685 14.009 5581 Z= 0.322 Chirality : 0.044 0.168 663 Planarity : 0.004 0.044 698 Dihedral : 5.247 55.804 631 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.53 % Rotamer: Outliers : 2.75 % Allowed : 25.62 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.37), residues: 547 helix: 1.67 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.38 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 389 TYR 0.012 0.001 TYR A 48 PHE 0.014 0.001 PHE A 34 TRP 0.006 0.001 TRP A 583 HIS 0.002 0.000 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4073) covalent geometry : angle 0.68486 / 0.32 ( 5566) SS BOND : bond 0.00204 / 0.12 ( 6) SS BOND : angle 0.58461 / 0.32 ( 12) hydrogen bonds : bond 0.03855 / 2.64 ( 272) hydrogen bonds : angle 4.31734 / 2.99 ( 801) link_NAG-ASN : bond 0.00417 / 0.22 ( 1) link_NAG-ASN : angle 1.18805 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.166 Fit side-chains REVERT: A 106 LEU cc_start: 0.8984 (mm) cc_final: 0.8326 (mm) REVERT: A 172 LEU cc_start: 0.8996 (tt) cc_final: 0.8754 (tt) REVERT: A 229 MET cc_start: 0.8048 (ptp) cc_final: 0.7688 (ptp) REVERT: A 257 TRP cc_start: 0.7185 (p-90) cc_final: 0.6342 (p-90) REVERT: A 311 PHE cc_start: 0.7581 (t80) cc_final: 0.6892 (m-80) REVERT: A 351 LYS cc_start: 0.6416 (mtpt) cc_final: 0.6174 (ttpt) REVERT: A 387 MET cc_start: 0.7062 (mmp) cc_final: 0.6849 (mmt) REVERT: A 409 MET cc_start: 0.7938 (mtt) cc_final: 0.7641 (mtt) REVERT: A 599 ASN cc_start: 0.6451 (m110) cc_final: 0.5845 (m110) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.0530 time to fit residues: 6.8938 Evaluate side-chains 101 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.139252 restraints weight = 6372.978| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.22 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4080 Z= 0.152 Angle : 0.721 13.697 5581 Z= 0.339 Chirality : 0.044 0.167 663 Planarity : 0.004 0.045 698 Dihedral : 5.304 58.112 631 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.53 % Rotamer: Outliers : 2.75 % Allowed : 26.17 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.37), residues: 547 helix: 1.64 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.34 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 561 TYR 0.010 0.001 TYR A 606 PHE 0.014 0.001 PHE A 34 TRP 0.009 0.001 TRP A 583 HIS 0.001 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4073) covalent geometry : angle 0.72123 / 0.34 ( 5566) SS BOND : bond 0.00226 / 0.12 ( 6) SS BOND : angle 0.63087 / 0.36 ( 12) hydrogen bonds : bond 0.04004 / 2.74 ( 272) hydrogen bonds : angle 4.35319 / 3.01 ( 801) link_NAG-ASN : bond 0.00427 / 0.22 ( 1) link_NAG-ASN : angle 1.13829 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9024 (mm) cc_final: 0.8387 (mm) REVERT: A 125 TYR cc_start: 0.7766 (p90) cc_final: 0.7539 (p90) REVERT: A 172 LEU cc_start: 0.9025 (tt) cc_final: 0.8793 (tt) REVERT: A 177 GLN cc_start: 0.8793 (tp40) cc_final: 0.8471 (tp40) REVERT: A 229 MET cc_start: 0.8029 (ptp) cc_final: 0.7652 (ptp) REVERT: A 257 TRP cc_start: 0.7203 (p-90) cc_final: 0.6341 (p-90) REVERT: A 311 PHE cc_start: 0.7563 (t80) cc_final: 0.6806 (m-80) REVERT: A 355 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7662 (mmmm) REVERT: A 387 MET cc_start: 0.7006 (mmp) cc_final: 0.6791 (mmt) REVERT: A 409 MET cc_start: 0.7943 (mtt) cc_final: 0.7659 (mtt) REVERT: A 599 ASN cc_start: 0.6439 (m110) cc_final: 0.5662 (m110) REVERT: A 606 TYR cc_start: 0.8129 (t80) cc_final: 0.7920 (t80) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.0584 time to fit residues: 7.3200 Evaluate side-chains 100 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.182755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141059 restraints weight = 6356.040| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.21 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4080 Z= 0.137 Angle : 0.701 15.071 5581 Z= 0.329 Chirality : 0.043 0.177 663 Planarity : 0.004 0.045 698 Dihedral : 5.260 59.342 631 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 2.48 % Allowed : 25.34 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.36), residues: 547 helix: 1.59 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -0.36 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 582 TYR 0.010 0.001 TYR A 223 PHE 0.016 0.001 PHE A 557 TRP 0.006 0.001 TRP A 583 HIS 0.001 0.000 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4073) covalent geometry : angle 0.70057 / 0.33 ( 5566) SS BOND : bond 0.00125 / 0.08 ( 6) SS BOND : angle 0.81379 / 0.45 ( 12) hydrogen bonds : bond 0.03938 / 2.67 ( 272) hydrogen bonds : angle 4.35091 / 3.01 ( 801) link_NAG-ASN : bond 0.00429 / 0.23 ( 1) link_NAG-ASN : angle 1.10274 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.084 Fit side-chains REVERT: A 62 ARG cc_start: 0.8866 (tpm170) cc_final: 0.8636 (tpm170) REVERT: A 85 ILE cc_start: 0.7778 (tt) cc_final: 0.7565 (tp) REVERT: A 106 LEU cc_start: 0.9041 (mm) cc_final: 0.8397 (mm) REVERT: A 172 LEU cc_start: 0.8996 (tt) cc_final: 0.8768 (tt) REVERT: A 177 GLN cc_start: 0.8746 (tp40) cc_final: 0.8486 (tp40) REVERT: A 229 MET cc_start: 0.8022 (ptp) cc_final: 0.7626 (ptp) REVERT: A 257 TRP cc_start: 0.7216 (p-90) cc_final: 0.6342 (p-90) REVERT: A 311 PHE cc_start: 0.7530 (t80) cc_final: 0.6793 (m-80) REVERT: A 387 MET cc_start: 0.7017 (mmp) cc_final: 0.6761 (mmt) REVERT: A 409 MET cc_start: 0.7900 (mtt) cc_final: 0.7632 (mtt) REVERT: A 599 ASN cc_start: 0.6574 (m110) cc_final: 0.5955 (m-40) REVERT: A 606 TYR cc_start: 0.8092 (t80) cc_final: 0.7886 (t80) outliers start: 9 outliers final: 8 residues processed: 98 average time/residue: 0.0480 time to fit residues: 5.9583 Evaluate side-chains 100 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.184129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141561 restraints weight = 6437.718| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 4.27 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4080 Z= 0.134 Angle : 0.712 15.159 5581 Z= 0.337 Chirality : 0.044 0.180 663 Planarity : 0.004 0.045 698 Dihedral : 5.263 59.222 631 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 1.93 % Allowed : 25.90 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.37), residues: 547 helix: 1.61 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.45 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 62 TYR 0.009 0.001 TYR A 48 PHE 0.019 0.001 PHE A 198 TRP 0.008 0.001 TRP A 253 HIS 0.002 0.000 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4073) covalent geometry : angle 0.71243 / 0.34 ( 5566) SS BOND : bond 0.00170 / 0.11 ( 6) SS BOND : angle 0.53330 / 0.30 ( 12) hydrogen bonds : bond 0.04044 / 2.74 ( 272) hydrogen bonds : angle 4.41210 / 3.04 ( 801) link_NAG-ASN : bond 0.00438 / 0.23 ( 1) link_NAG-ASN : angle 1.09624 / 0.57 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.142 Fit side-chains REVERT: A 85 ILE cc_start: 0.7768 (tt) cc_final: 0.7559 (tp) REVERT: A 106 LEU cc_start: 0.9030 (mm) cc_final: 0.8356 (mm) REVERT: A 172 LEU cc_start: 0.8994 (tt) cc_final: 0.8773 (tt) REVERT: A 177 GLN cc_start: 0.8747 (tp40) cc_final: 0.8496 (tp40) REVERT: A 229 MET cc_start: 0.8022 (ptp) cc_final: 0.7625 (ptp) REVERT: A 257 TRP cc_start: 0.7218 (p-90) cc_final: 0.6326 (p-90) REVERT: A 311 PHE cc_start: 0.7591 (t80) cc_final: 0.6861 (m-80) REVERT: A 387 MET cc_start: 0.7073 (mmp) cc_final: 0.6830 (mmt) REVERT: A 409 MET cc_start: 0.7877 (mtt) cc_final: 0.7614 (mtt) REVERT: A 605 ARG cc_start: 0.7178 (mmp-170) cc_final: 0.6970 (mmp-170) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.0588 time to fit residues: 7.0694 Evaluate side-chains 97 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 40.0000 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.184622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.141931 restraints weight = 6504.117| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.30 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4080 Z= 0.137 Angle : 0.718 15.011 5581 Z= 0.339 Chirality : 0.044 0.185 663 Planarity : 0.004 0.046 698 Dihedral : 5.125 57.200 631 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.53 % Rotamer: Outliers : 1.65 % Allowed : 26.72 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.37), residues: 547 helix: 1.66 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.36 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.010 0.001 TYR A 223 PHE 0.023 0.001 PHE A 198 TRP 0.008 0.001 TRP A 583 HIS 0.001 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 4073) covalent geometry : angle 0.71842 / 0.34 ( 5566) SS BOND : bond 0.00214 / 0.13 ( 6) SS BOND : angle 0.56878 / 0.32 ( 12) hydrogen bonds : bond 0.04000 / 2.71 ( 272) hydrogen bonds : angle 4.38793 / 3.01 ( 801) link_NAG-ASN : bond 0.00430 / 0.23 ( 1) link_NAG-ASN : angle 1.08302 / 0.57 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 795.71 seconds wall clock time: 14 minutes 19.08 seconds (859.08 seconds total)