Starting phenix.real_space_refine on Tue Mar 3 12:41:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r0n_53485/03_2026/9r0n_53485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r0n_53485/03_2026/9r0n_53485.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9r0n_53485/03_2026/9r0n_53485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r0n_53485/03_2026/9r0n_53485.map" model { file = "/net/cci-nas-00/data/ceres_data/9r0n_53485/03_2026/9r0n_53485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r0n_53485/03_2026/9r0n_53485.cif" } 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= -0.000 sd= 0.008 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 35 5.16 5 C 2820 2.51 5 N 686 2.21 5 O 746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4287 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4227 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'UGU': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.21, per 1000 atoms: 0.28 Number of scatterers: 4287 At special positions: 0 Unit cell: (86.376, 96.624, 73.932, 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 35 16.00 O 746 8.00 N 686 7.00 C 2820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.04 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=2.05 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 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 401.4 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 71.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 3.657A pdb=" N ASN A 30 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 64 removed outlier: 4.704A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 92 removed outlier: 4.158A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.737A pdb=" N PHE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.715A pdb=" N VAL A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.635A pdb=" N SER A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.508A pdb=" N ALA A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.961A pdb=" N ARG A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.550A pdb=" N THR A 243 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.633A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 324 through 357 removed outlier: 3.594A pdb=" N THR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 370 Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.529A pdb=" N LEU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 4.369A pdb=" N ARG A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 514 through 532 removed outlier: 4.023A pdb=" N SER A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.798A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 566 through 578 removed outlier: 4.297A pdb=" N SER A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 460 removed outlier: 4.176A pdb=" N SER A 476 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.708A pdb=" N TYR A 596 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 583 " --> pdb=" O CYS A 594 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS A 594 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR A 585 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY A 592 " --> pdb=" O TYR A 585 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 813 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: 0.83 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 844 1.33 - 1.47: 1574 1.47 - 1.60: 1932 1.60 - 1.74: 0 1.74 - 1.87: 51 Bond restraints: 4401 Sorted by residual: bond pdb=" CB CYS A 492 " pdb=" SG CYS A 492 " ideal model delta sigma weight residual 1.808 1.871 -0.063 3.30e-02 9.18e+02 3.60e+00 bond pdb=" N SER A 26 " pdb=" CA SER A 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" CAJ Y01 A 702 " pdb=" CAN Y01 A 702 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" CAV Y01 A 702 " pdb=" CBC Y01 A 702 " ideal model delta sigma weight residual 1.523 1.492 0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" CAJ Y01 A 702 " pdb=" CAO Y01 A 702 " ideal model delta sigma weight residual 1.526 1.495 0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5779 1.35 - 2.71: 147 2.71 - 4.06: 45 4.06 - 5.41: 11 5.41 - 6.77: 3 Bond angle restraints: 5985 Sorted by residual: angle pdb=" CA CYS A 494 " pdb=" CB CYS A 494 " pdb=" SG CYS A 494 " ideal model delta sigma weight residual 114.40 121.17 -6.77 2.30e+00 1.89e-01 8.65e+00 angle pdb=" C11 UGU A 701 " pdb=" C12 UGU A 701 " pdb=" C13 UGU A 701 " ideal model delta sigma weight residual 117.79 111.51 6.28 3.00e+00 1.11e-01 4.39e+00 angle pdb=" N CYS A 474 " pdb=" CA CYS A 474 " pdb=" C CYS A 474 " ideal model delta sigma weight residual 110.20 113.46 -3.26 1.58e+00 4.01e-01 4.26e+00 angle pdb=" N VAL A 495 " pdb=" CA VAL A 495 " pdb=" C VAL A 495 " ideal model delta sigma weight residual 109.34 105.37 3.97 2.08e+00 2.31e-01 3.65e+00 angle pdb=" CB MET A 328 " pdb=" CG MET A 328 " pdb=" SD MET A 328 " ideal model delta sigma weight residual 112.70 118.27 -5.57 3.00e+00 1.11e-01 3.44e+00 ... (remaining 5980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.99: 2497 23.99 - 47.98: 154 47.98 - 71.96: 22 71.96 - 95.95: 2 95.95 - 119.94: 2 Dihedral angle restraints: 2677 sinusoidal: 1089 harmonic: 1588 Sorted by residual: dihedral pdb=" CB CYS A 444 " pdb=" SG CYS A 444 " pdb=" SG CYS A 494 " pdb=" CB CYS A 494 " ideal model delta sinusoidal sigma weight residual 93.00 24.86 68.14 1 1.00e+01 1.00e-02 6.03e+01 dihedral pdb=" CA CYS A 494 " pdb=" C CYS A 494 " pdb=" N VAL A 495 " pdb=" CA VAL A 495 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA CYS A 492 " pdb=" C CYS A 492 " pdb=" N SER A 493 " pdb=" CA SER A 493 " ideal model delta harmonic sigma weight residual 180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 2674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 615 0.063 - 0.125: 70 0.125 - 0.188: 5 0.188 - 0.250: 0 0.250 - 0.313: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" C12 UGU A 701 " pdb=" C11 UGU A 701 " pdb=" C13 UGU A 701 " pdb=" C8 UGU A 701 " both_signs ideal model delta sigma weight residual False 2.42 2.74 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL A 495 " pdb=" N VAL A 495 " pdb=" C VAL A 495 " pdb=" CB VAL A 495 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" C8 UGU A 701 " pdb=" C12 UGU A 701 " pdb=" C7 UGU A 701 " pdb=" C9 UGU A 701 " both_signs ideal model delta sigma weight residual False -2.54 -2.69 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 688 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 372 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 373 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 516 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 517 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 247 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 248 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.018 5.00e-02 4.00e+02 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1814 2.92 - 3.41: 4521 3.41 - 3.91: 6866 3.91 - 4.40: 7878 4.40 - 4.90: 13166 Nonbonded interactions: 34245 Sorted by model distance: nonbonded pdb=" O ARG A 445 " pdb=" O CYS A 448 " model vdw 2.422 3.040 nonbonded pdb=" O SER A 75 " pdb=" OE1 GLU A 78 " model vdw 2.472 3.040 nonbonded pdb=" O THR A 479 " pdb=" OG1 THR A 479 " model vdw 2.535 3.040 nonbonded pdb=" O ALA A 601 " pdb=" OD1 ASN A 604 " model vdw 2.559 3.040 nonbonded pdb=" OH TYR A 356 " pdb=" OG SER A 518 " model vdw 2.571 3.040 ... (remaining 34240 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: 7.430 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.870 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4407 Z= 0.173 Angle : 0.605 7.004 5997 Z= 0.294 Chirality : 0.042 0.313 691 Planarity : 0.004 0.037 739 Dihedral : 15.149 119.937 1639 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.07 % Allowed : 12.42 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.93 (0.36), residues: 543 helix: 1.84 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.36 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.013 0.001 TYR A 51 PHE 0.008 0.001 PHE A 113 TRP 0.006 0.001 TRP A 253 HIS 0.005 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4401) covalent geometry : angle 0.59749 ( 5985) SS BOND : bond 0.00998 ( 6) SS BOND : angle 2.17190 ( 12) hydrogen bonds : bond 0.13803 ( 275) hydrogen bonds : angle 6.28543 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.166 Fit side-chains REVERT: A 200 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6136 (tp30) REVERT: A 201 PRO cc_start: 0.7794 (Cg_exo) cc_final: 0.7221 (Cg_endo) REVERT: A 454 PHE cc_start: 0.7635 (m-80) cc_final: 0.7115 (m-80) outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.0685 time to fit residues: 6.6614 Evaluate side-chains 56 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 424 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.105325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085265 restraints weight = 10485.686| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.04 r_work: 0.3171 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4407 Z= 0.129 Angle : 0.596 7.453 5997 Z= 0.285 Chirality : 0.043 0.248 691 Planarity : 0.004 0.036 739 Dihedral : 9.462 96.387 701 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.57 % Allowed : 12.63 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.57 (0.36), residues: 543 helix: 2.31 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 0.59 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.011 0.001 TYR A 606 PHE 0.011 0.001 PHE A 217 TRP 0.005 0.001 TRP A 583 HIS 0.001 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4401) covalent geometry : angle 0.59264 ( 5985) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.50432 ( 12) hydrogen bonds : bond 0.04329 ( 275) hydrogen bonds : angle 4.48689 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8246 (tt0) cc_final: 0.7945 (tt0) REVERT: A 74 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8706 (p) REVERT: A 201 PRO cc_start: 0.8659 (Cg_exo) cc_final: 0.8378 (Cg_endo) REVERT: A 454 PHE cc_start: 0.7789 (m-80) cc_final: 0.6840 (m-80) outliers start: 12 outliers final: 3 residues processed: 71 average time/residue: 0.0583 time to fit residues: 5.6274 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 450 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.103792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083400 restraints weight = 10360.933| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.05 r_work: 0.3181 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4407 Z= 0.128 Angle : 0.564 6.919 5997 Z= 0.270 Chirality : 0.043 0.255 691 Planarity : 0.004 0.035 739 Dihedral : 8.830 97.929 697 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 4.07 % Allowed : 13.28 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.80 (0.35), residues: 543 helix: 2.45 (0.26), residues: 358 sheet: None (None), residues: 0 loop : 0.75 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.012 0.001 TYR A 606 PHE 0.011 0.001 PHE A 524 TRP 0.004 0.001 TRP A 253 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4401) covalent geometry : angle 0.55837 ( 5985) SS BOND : bond 0.00706 ( 6) SS BOND : angle 1.83410 ( 12) hydrogen bonds : bond 0.03963 ( 275) hydrogen bonds : angle 4.29016 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8288 (tt0) cc_final: 0.7963 (tt0) REVERT: A 308 MET cc_start: 0.7498 (tmm) cc_final: 0.7296 (tmm) REVERT: A 410 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 454 PHE cc_start: 0.7867 (m-80) cc_final: 0.6900 (m-80) REVERT: A 628 MET cc_start: 0.9216 (mtp) cc_final: 0.8970 (mtp) outliers start: 19 outliers final: 10 residues processed: 72 average time/residue: 0.0554 time to fit residues: 5.4199 Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084702 restraints weight = 10521.378| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.02 r_work: 0.3165 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4407 Z= 0.136 Angle : 0.558 6.424 5997 Z= 0.268 Chirality : 0.043 0.236 691 Planarity : 0.004 0.032 739 Dihedral : 8.549 96.279 697 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 4.28 % Allowed : 14.13 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.06 (0.36), residues: 543 helix: 2.63 (0.26), residues: 358 sheet: None (None), residues: 0 loop : 0.93 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.012 0.001 TYR A 606 PHE 0.026 0.001 PHE A 557 TRP 0.003 0.001 TRP A 253 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4401) covalent geometry : angle 0.55083 ( 5985) SS BOND : bond 0.00630 ( 6) SS BOND : angle 2.04712 ( 12) hydrogen bonds : bond 0.03792 ( 275) hydrogen bonds : angle 4.14325 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8344 (tt0) cc_final: 0.7997 (tt0) REVERT: A 74 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8719 (p) REVERT: A 308 MET cc_start: 0.7477 (tmm) cc_final: 0.6712 (tpt) REVERT: A 454 PHE cc_start: 0.7947 (m-80) cc_final: 0.6964 (m-80) outliers start: 20 outliers final: 14 residues processed: 70 average time/residue: 0.0475 time to fit residues: 4.7008 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 616 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084935 restraints weight = 10522.641| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.06 r_work: 0.3154 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4407 Z= 0.123 Angle : 0.551 6.669 5997 Z= 0.260 Chirality : 0.042 0.225 691 Planarity : 0.004 0.033 739 Dihedral : 8.004 91.517 697 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 4.50 % Allowed : 14.35 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.20 (0.36), residues: 543 helix: 2.73 (0.26), residues: 358 sheet: None (None), residues: 0 loop : 1.00 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.011 0.001 TYR A 606 PHE 0.015 0.001 PHE A 337 TRP 0.005 0.001 TRP A 626 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4401) covalent geometry : angle 0.54786 ( 5985) SS BOND : bond 0.00449 ( 6) SS BOND : angle 1.40987 ( 12) hydrogen bonds : bond 0.03612 ( 275) hydrogen bonds : angle 4.04687 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8340 (tt0) cc_final: 0.7985 (tt0) REVERT: A 74 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8736 (p) REVERT: A 308 MET cc_start: 0.7523 (tmm) cc_final: 0.6724 (tpt) REVERT: A 321 LEU cc_start: 0.9167 (tp) cc_final: 0.8858 (tp) REVERT: A 379 MET cc_start: 0.9025 (mmt) cc_final: 0.8761 (mmt) REVERT: A 454 PHE cc_start: 0.7939 (m-80) cc_final: 0.6919 (m-80) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.0572 time to fit residues: 5.9348 Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082474 restraints weight = 10757.682| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.28 r_work: 0.3137 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 4407 Z= 0.109 Angle : 0.541 6.038 5997 Z= 0.256 Chirality : 0.042 0.214 691 Planarity : 0.003 0.033 739 Dihedral : 6.586 59.260 697 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.29 % Favored : 98.53 % Rotamer: Outliers : 3.43 % Allowed : 16.49 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.31 (0.36), residues: 543 helix: 2.84 (0.26), residues: 357 sheet: None (None), residues: 0 loop : 0.99 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.010 0.001 TYR A 606 PHE 0.010 0.001 PHE A 337 TRP 0.008 0.001 TRP A 626 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4401) covalent geometry : angle 0.53547 ( 5985) SS BOND : bond 0.00766 ( 6) SS BOND : angle 1.73635 ( 12) hydrogen bonds : bond 0.03409 ( 275) hydrogen bonds : angle 3.97828 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8383 (tt0) cc_final: 0.8024 (tt0) REVERT: A 74 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 308 MET cc_start: 0.7536 (tmm) cc_final: 0.6730 (tpt) REVERT: A 321 LEU cc_start: 0.9165 (tp) cc_final: 0.8864 (tp) REVERT: A 379 MET cc_start: 0.9031 (mmt) cc_final: 0.8788 (mmt) REVERT: A 454 PHE cc_start: 0.7950 (m-80) cc_final: 0.6943 (m-80) outliers start: 16 outliers final: 13 residues processed: 76 average time/residue: 0.0606 time to fit residues: 6.0016 Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 562 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082184 restraints weight = 10673.626| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.19 r_work: 0.3115 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4407 Z= 0.144 Angle : 0.572 6.228 5997 Z= 0.270 Chirality : 0.043 0.224 691 Planarity : 0.003 0.030 739 Dihedral : 6.160 49.937 696 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 4.28 % Allowed : 16.70 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.25 (0.36), residues: 543 helix: 2.78 (0.26), residues: 358 sheet: None (None), residues: 0 loop : 0.99 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.011 0.001 TYR A 606 PHE 0.009 0.001 PHE A 52 TRP 0.006 0.001 TRP A 626 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4401) covalent geometry : angle 0.56845 ( 5985) SS BOND : bond 0.00579 ( 6) SS BOND : angle 1.46160 ( 12) hydrogen bonds : bond 0.03636 ( 275) hydrogen bonds : angle 4.03649 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.169 Fit side-chains REVERT: A 60 GLU cc_start: 0.8433 (tt0) cc_final: 0.8085 (tt0) REVERT: A 74 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8683 (p) REVERT: A 308 MET cc_start: 0.7592 (tmm) cc_final: 0.7330 (tmm) REVERT: A 321 LEU cc_start: 0.9205 (tp) cc_final: 0.8925 (tp) REVERT: A 379 MET cc_start: 0.9024 (mmt) cc_final: 0.8749 (mmt) REVERT: A 454 PHE cc_start: 0.7965 (m-80) cc_final: 0.6962 (m-80) outliers start: 20 outliers final: 15 residues processed: 70 average time/residue: 0.0559 time to fit residues: 5.2550 Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 33 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.0020 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083974 restraints weight = 10588.962| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.25 r_work: 0.3147 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4407 Z= 0.104 Angle : 0.557 7.106 5997 Z= 0.262 Chirality : 0.042 0.209 691 Planarity : 0.004 0.032 739 Dihedral : 5.893 45.847 696 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.29 % Favored : 98.53 % Rotamer: Outliers : 3.00 % Allowed : 17.56 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.33 (0.36), residues: 543 helix: 2.87 (0.26), residues: 357 sheet: None (None), residues: 0 loop : 0.95 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.009 0.001 TYR A 606 PHE 0.009 0.001 PHE A 524 TRP 0.005 0.001 TRP A 626 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 4401) covalent geometry : angle 0.55494 ( 5985) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.26061 ( 12) hydrogen bonds : bond 0.03360 ( 275) hydrogen bonds : angle 3.96517 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8381 (tt0) cc_final: 0.7999 (tt0) REVERT: A 74 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8824 (p) REVERT: A 308 MET cc_start: 0.7558 (tmm) cc_final: 0.6736 (tpt) REVERT: A 321 LEU cc_start: 0.9180 (tp) cc_final: 0.8894 (tp) REVERT: A 379 MET cc_start: 0.9002 (mmt) cc_final: 0.8773 (mmt) REVERT: A 454 PHE cc_start: 0.7968 (m-80) cc_final: 0.6946 (m-80) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.0460 time to fit residues: 4.5965 Evaluate side-chains 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082880 restraints weight = 10640.056| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.17 r_work: 0.3128 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4407 Z= 0.132 Angle : 0.604 13.321 5997 Z= 0.279 Chirality : 0.043 0.218 691 Planarity : 0.003 0.030 739 Dihedral : 5.874 45.597 696 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 4.07 % Allowed : 16.70 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.35 (0.36), residues: 543 helix: 2.89 (0.26), residues: 357 sheet: None (None), residues: 0 loop : 0.97 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.010 0.001 TYR A 606 PHE 0.009 0.001 PHE A 52 TRP 0.005 0.001 TRP A 626 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4401) covalent geometry : angle 0.60252 ( 5985) SS BOND : bond 0.00405 ( 6) SS BOND : angle 1.16186 ( 12) hydrogen bonds : bond 0.03562 ( 275) hydrogen bonds : angle 4.03887 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8411 (tt0) cc_final: 0.8050 (tt0) REVERT: A 74 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8760 (p) REVERT: A 308 MET cc_start: 0.7622 (tmm) cc_final: 0.7360 (tmm) REVERT: A 321 LEU cc_start: 0.9221 (tp) cc_final: 0.8950 (tp) REVERT: A 379 MET cc_start: 0.8993 (mmt) cc_final: 0.8740 (mmt) REVERT: A 454 PHE cc_start: 0.7968 (m-80) cc_final: 0.6953 (m-80) outliers start: 19 outliers final: 13 residues processed: 73 average time/residue: 0.0501 time to fit residues: 4.8663 Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.0050 chunk 0 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.083040 restraints weight = 10668.292| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.24 r_work: 0.3131 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4407 Z= 0.118 Angle : 0.603 13.421 5997 Z= 0.281 Chirality : 0.043 0.213 691 Planarity : 0.003 0.030 739 Dihedral : 5.821 46.013 696 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.29 % Favored : 98.53 % Rotamer: Outliers : 2.78 % Allowed : 18.20 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.33 (0.36), residues: 543 helix: 2.88 (0.26), residues: 357 sheet: None (None), residues: 0 loop : 0.95 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.010 0.001 TYR A 606 PHE 0.008 0.001 PHE A 267 TRP 0.004 0.001 TRP A 626 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4401) covalent geometry : angle 0.60113 ( 5985) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.14879 ( 12) hydrogen bonds : bond 0.03487 ( 275) hydrogen bonds : angle 4.02051 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8409 (tt0) cc_final: 0.8047 (tt0) REVERT: A 74 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 308 MET cc_start: 0.7613 (tmm) cc_final: 0.6795 (tpt) REVERT: A 321 LEU cc_start: 0.9210 (tp) cc_final: 0.8942 (tp) REVERT: A 454 PHE cc_start: 0.7958 (m-80) cc_final: 0.6946 (m-80) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 0.0558 time to fit residues: 5.1331 Evaluate side-chains 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083983 restraints weight = 10535.893| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.12 r_work: 0.3150 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4407 Z= 0.110 Angle : 0.587 13.474 5997 Z= 0.271 Chirality : 0.043 0.211 691 Planarity : 0.003 0.030 739 Dihedral : 5.748 46.406 696 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.66 % Favored : 98.16 % Rotamer: Outliers : 2.78 % Allowed : 18.20 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 3.32 (0.36), residues: 543 helix: 2.87 (0.26), residues: 357 sheet: None (None), residues: 0 loop : 0.96 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.009 0.001 TYR A 606 PHE 0.008 0.001 PHE A 52 TRP 0.004 0.001 TRP A 626 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4401) covalent geometry : angle 0.58590 ( 5985) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.04953 ( 12) hydrogen bonds : bond 0.03455 ( 275) hydrogen bonds : angle 4.01484 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1108.47 seconds wall clock time: 19 minutes 44.62 seconds (1184.62 seconds total)