Starting phenix.real_space_refine on Tue Aug 4 15:40:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wc6_65856/08_2026/9wc6_65856_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wc6_65856/08_2026/9wc6_65856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wc6_65856/08_2026/9wc6_65856_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wc6_65856/08_2026/9wc6_65856_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wc6_65856/08_2026/9wc6_65856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wc6_65856/08_2026/9wc6_65856.map" } resolution = 3.1 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= -0.003 sd= 0.111 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2946 2.51 5 N 671 2.21 5 O 728 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: 4381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4373 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 31, 'TRANS': 525} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' CL': 1, ' NA': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 1.16, per 1000 atoms: 0.26 Number of scatterers: 4381 At special positions: 0 Unit cell: (80.025, 62.953, 91.762, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 728 8.00 N 671 7.00 C 2946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.32 Conformation dependent library (CDL) restraints added in 124.1 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 78.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.586A pdb=" N VAL A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.524A pdb=" N TYR A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 241 through 256 Processing helix chain 'A' and resid 260 through 265 removed outlier: 3.856A pdb=" N LYS A 264 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 300 removed outlier: 4.031A pdb=" N MET A 276 " --> pdb=" O CYS A 272 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.712A pdb=" N SER A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 393 through 414 Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 445 through 455 removed outlier: 4.086A pdb=" N GLY A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.831A pdb=" N TRP A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 483 through 491 removed outlier: 4.029A pdb=" N TYR A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 532 Processing helix chain 'A' and resid 544 through 557 Proline residue: A 551 - end of helix removed outlier: 3.827A pdb=" N ARG A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 594 removed outlier: 3.661A pdb=" N THR A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 617 Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 622 through 623 No H-bonds generated for 'chain 'A' and resid 622 through 623' Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.654A pdb=" N MET A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 654 Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 683 through 699 Processing helix chain 'A' and resid 711 through 727 removed outlier: 3.722A pdb=" N MET A 715 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 743 through 753 Processing helix chain 'A' and resid 767 through 771 removed outlier: 3.566A pdb=" N TYR A 770 " --> pdb=" O GLY A 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 704 through 705 289 hydrogen bonds defined for protein. 852 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: 0.60 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1249 1.34 - 1.46: 905 1.46 - 1.58: 2315 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4520 Sorted by residual: bond pdb=" N ASN A 193 " pdb=" CA ASN A 193 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.09e-02 8.42e+03 9.57e+00 bond pdb=" N ILE A 514 " pdb=" CA ILE A 514 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.42e+00 bond pdb=" N ILE A 474 " pdb=" CA ILE A 474 " ideal model delta sigma weight residual 1.460 1.494 -0.033 1.26e-02 6.30e+03 7.03e+00 bond pdb=" N ASN A 213 " pdb=" CA ASN A 213 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.28e-02 6.10e+03 6.40e+00 ... (remaining 4515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 5823 1.31 - 2.63: 256 2.63 - 3.94: 70 3.94 - 5.26: 15 5.26 - 6.57: 8 Bond angle restraints: 6172 Sorted by residual: angle pdb=" N ALA A 412 " pdb=" CA ALA A 412 " pdb=" C ALA A 412 " ideal model delta sigma weight residual 111.36 106.88 4.48 1.09e+00 8.42e-01 1.69e+01 angle pdb=" C CYS A 311 " pdb=" CA CYS A 311 " pdb=" CB CYS A 311 " ideal model delta sigma weight residual 111.28 105.18 6.10 1.58e+00 4.01e-01 1.49e+01 angle pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" O SER A 477 " ideal model delta sigma weight residual 121.99 117.72 4.27 1.14e+00 7.69e-01 1.40e+01 angle pdb=" N ILE A 382 " pdb=" CA ILE A 382 " pdb=" C ILE A 382 " ideal model delta sigma weight residual 109.37 114.30 -4.93 1.35e+00 5.49e-01 1.33e+01 angle pdb=" N SER A 477 " pdb=" CA SER A 477 " pdb=" C SER A 477 " ideal model delta sigma weight residual 110.41 106.01 4.40 1.23e+00 6.61e-01 1.28e+01 ... (remaining 6167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 2208 16.14 - 32.27: 266 32.27 - 48.41: 72 48.41 - 64.55: 13 64.55 - 80.68: 2 Dihedral angle restraints: 2561 sinusoidal: 950 harmonic: 1611 Sorted by residual: dihedral pdb=" CA PHE A 683 " pdb=" C PHE A 683 " pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LYS A 381 " pdb=" C LYS A 381 " pdb=" N ILE A 382 " pdb=" CA ILE A 382 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA TRP A 263 " pdb=" C TRP A 263 " pdb=" N LYS A 264 " pdb=" CA LYS A 264 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 2558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 571 0.059 - 0.117: 112 0.117 - 0.175: 7 0.175 - 0.234: 6 0.234 - 0.292: 1 Chirality restraints: 697 Sorted by residual: chirality pdb=" CA TRP A 263 " pdb=" N TRP A 263 " pdb=" C TRP A 263 " pdb=" CB TRP A 263 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL A 421 " pdb=" N VAL A 421 " pdb=" C VAL A 421 " pdb=" CB VAL A 421 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 514 " pdb=" N ILE A 514 " pdb=" C ILE A 514 " pdb=" CB ILE A 514 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 694 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 191 " 0.250 9.50e-02 1.11e+02 1.12e-01 7.71e+00 pdb=" NE ARG A 191 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 191 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 191 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 191 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 476 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE A 476 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE A 476 " -0.017 2.00e-02 2.50e+03 pdb=" N SER A 477 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 491 " -0.020 2.00e-02 2.50e+03 1.70e-02 5.80e+00 pdb=" CG TYR A 491 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 491 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 491 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 491 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 491 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 491 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR A 491 " 0.004 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 10 2.49 - 3.09: 3287 3.09 - 3.70: 7081 3.70 - 4.30: 10246 4.30 - 4.90: 17102 Nonbonded interactions: 37726 Sorted by model distance: nonbonded pdb=" CB SER A 477 " pdb="NA NA A 803 " model vdw 1.889 2.870 nonbonded pdb=" O THR A 588 " pdb=" OD1 ASP A 592 " model vdw 2.280 3.040 nonbonded pdb=" O GLY A 206 " pdb="NA NA A 802 " model vdw 2.350 2.470 nonbonded pdb=" O LEU A 574 " pdb="NA NA A 802 " model vdw 2.351 2.470 nonbonded pdb=" CA SER A 477 " pdb="NA NA A 803 " model vdw 2.358 2.900 ... (remaining 37721 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: 1.330 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.290 Find NCS groups from input model: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.006 0.037 4520 Z= 0.294 Angle : 0.692 6.572 6172 Z= 0.413 Chirality : 0.049 0.292 697 Planarity : 0.006 0.112 748 Dihedral : 15.138 80.682 1531 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 20.43 % Favored : 79.57 % 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: 0.38 (0.34), residues: 551 helix: 0.76 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.73 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 709 TYR 0.036 0.002 TYR A 491 PHE 0.011 0.001 PHE A 568 TRP 0.009 0.001 TRP A 315 HIS 0.001 0.000 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.29 ( 4520) covalent geometry : angle 0.69177 / 0.41 ( 6172) hydrogen bonds : bond 0.18989 / 12.46 ( 289) hydrogen bonds : angle 7.23244 / 4.89 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.124 Fit side-chains REVERT: A 249 VAL cc_start: 0.8797 (t) cc_final: 0.8532 (m) REVERT: A 319 GLU cc_start: 0.7881 (mp0) cc_final: 0.7633 (mp0) REVERT: A 398 LEU cc_start: 0.8690 (tm) cc_final: 0.8412 (tp) REVERT: A 430 TYR cc_start: 0.8192 (m-80) cc_final: 0.7624 (m-80) REVERT: A 431 VAL cc_start: 0.8730 (p) cc_final: 0.8491 (m) REVERT: A 584 GLU cc_start: 0.8638 (tp30) cc_final: 0.8416 (tp30) REVERT: A 647 PHE cc_start: 0.9035 (m-80) cc_final: 0.8833 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0496 time to fit residues: 6.3179 Evaluate side-chains 87 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117170 restraints weight = 5723.207| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.64 r_work: 0.3210 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4520 Z= 0.137 Angle : 0.548 5.709 6172 Z= 0.285 Chirality : 0.041 0.126 697 Planarity : 0.005 0.035 748 Dihedral : 5.428 83.429 595 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.39 % Allowed : 18.04 % Favored : 79.57 % 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: 1.26 (0.35), residues: 551 helix: 1.28 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.06 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 766 TYR 0.020 0.001 TYR A 219 PHE 0.021 0.001 PHE A 475 TRP 0.005 0.001 TRP A 713 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4520) covalent geometry : angle 0.54840 / 0.29 ( 6172) hydrogen bonds : bond 0.04449 / 2.91 ( 289) hydrogen bonds : angle 4.62981 / 3.16 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.160 Fit side-chains REVERT: A 201 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8791 (mt) REVERT: A 247 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8853 (tp) REVERT: A 398 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8363 (tp) REVERT: A 431 VAL cc_start: 0.8810 (p) cc_final: 0.8469 (m) REVERT: A 538 VAL cc_start: 0.8839 (p) cc_final: 0.8632 (t) REVERT: A 584 GLU cc_start: 0.8325 (tp30) cc_final: 0.7990 (tp30) outliers start: 11 outliers final: 5 residues processed: 92 average time/residue: 0.0479 time to fit residues: 6.3260 Evaluate side-chains 90 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN A 492 ASN A 496 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116603 restraints weight = 5634.912| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.63 r_work: 0.3237 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4520 Z= 0.143 Angle : 0.531 6.132 6172 Z= 0.273 Chirality : 0.041 0.127 697 Planarity : 0.004 0.035 748 Dihedral : 5.274 81.530 595 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.13 % Allowed : 15.43 % Favored : 80.43 % 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: 1.39 (0.35), residues: 551 helix: 1.43 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.18 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.021 0.001 TYR A 219 PHE 0.016 0.001 PHE A 475 TRP 0.011 0.001 TRP A 728 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4520) covalent geometry : angle 0.53074 / 0.27 ( 6172) hydrogen bonds : bond 0.04219 / 2.75 ( 289) hydrogen bonds : angle 4.44358 / 3.02 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.155 Fit side-chains REVERT: A 201 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 219 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.5991 (p90) REVERT: A 247 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8807 (tp) REVERT: A 398 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 424 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7397 (t80) REVERT: A 430 TYR cc_start: 0.8031 (m-80) cc_final: 0.7609 (m-80) REVERT: A 431 VAL cc_start: 0.8756 (p) cc_final: 0.8405 (m) REVERT: A 584 GLU cc_start: 0.8396 (tp30) cc_final: 0.8064 (tp30) outliers start: 19 outliers final: 8 residues processed: 100 average time/residue: 0.0466 time to fit residues: 6.6808 Evaluate side-chains 98 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 11 optimal weight: 0.2980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117854 restraints weight = 5628.547| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.66 r_work: 0.3184 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4520 Z= 0.135 Angle : 0.520 7.185 6172 Z= 0.269 Chirality : 0.041 0.126 697 Planarity : 0.004 0.034 748 Dihedral : 5.219 80.803 595 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.70 % Allowed : 17.39 % Favored : 78.91 % 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 (0.35), residues: 551 helix: 1.52 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.19 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.020 0.001 TYR A 219 PHE 0.014 0.001 PHE A 475 TRP 0.010 0.001 TRP A 728 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4520) covalent geometry : angle 0.51981 / 0.27 ( 6172) hydrogen bonds : bond 0.03920 / 2.56 ( 289) hydrogen bonds : angle 4.30663 / 2.93 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.189 Fit side-chains REVERT: A 219 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.6019 (p90) REVERT: A 381 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8466 (mmmt) REVERT: A 398 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 424 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7299 (t80) REVERT: A 430 TYR cc_start: 0.8020 (m-80) cc_final: 0.7581 (m-80) REVERT: A 431 VAL cc_start: 0.8702 (p) cc_final: 0.8354 (m) REVERT: A 584 GLU cc_start: 0.8409 (tp30) cc_final: 0.8093 (tp30) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 0.0505 time to fit residues: 6.9784 Evaluate side-chains 100 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117865 restraints weight = 5623.342| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.64 r_work: 0.3114 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4520 Z= 0.137 Angle : 0.524 7.780 6172 Z= 0.269 Chirality : 0.041 0.126 697 Planarity : 0.004 0.034 748 Dihedral : 5.177 79.884 595 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.35 % Allowed : 17.39 % Favored : 78.26 % 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 (0.35), residues: 551 helix: 1.59 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.14 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.022 0.001 TYR A 219 PHE 0.014 0.001 PHE A 695 TRP 0.010 0.001 TRP A 467 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4520) covalent geometry : angle 0.52377 / 0.27 ( 6172) hydrogen bonds : bond 0.03887 / 2.54 ( 289) hydrogen bonds : angle 4.27249 / 2.88 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.165 Fit side-chains REVERT: A 219 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.6093 (p90) REVERT: A 398 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8238 (tp) REVERT: A 424 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7182 (t80) REVERT: A 431 VAL cc_start: 0.8657 (p) cc_final: 0.8318 (m) REVERT: A 584 GLU cc_start: 0.8373 (tp30) cc_final: 0.7967 (tp30) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 0.0434 time to fit residues: 6.2330 Evaluate side-chains 101 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118793 restraints weight = 5623.359| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.59 r_work: 0.3165 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4520 Z= 0.128 Angle : 0.516 8.174 6172 Z= 0.265 Chirality : 0.041 0.125 697 Planarity : 0.004 0.033 748 Dihedral : 5.120 78.143 595 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.48 % Allowed : 18.04 % Favored : 78.48 % 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: 1.64 (0.35), residues: 551 helix: 1.65 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.17 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.022 0.001 TYR A 219 PHE 0.013 0.001 PHE A 475 TRP 0.007 0.001 TRP A 713 HIS 0.000 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4520) covalent geometry : angle 0.51634 / 0.26 ( 6172) hydrogen bonds : bond 0.03771 / 2.47 ( 289) hydrogen bonds : angle 4.22838 / 2.85 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.100 Fit side-chains REVERT: A 219 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.6043 (p90) REVERT: A 319 GLU cc_start: 0.8093 (mp0) cc_final: 0.7526 (mp0) REVERT: A 381 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8472 (mmmm) REVERT: A 387 GLU cc_start: 0.9078 (pm20) cc_final: 0.8742 (pm20) REVERT: A 398 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 424 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7096 (t80) REVERT: A 431 VAL cc_start: 0.8666 (p) cc_final: 0.8318 (m) REVERT: A 584 GLU cc_start: 0.8370 (tp30) cc_final: 0.8000 (tp30) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 0.0421 time to fit residues: 5.7313 Evaluate side-chains 102 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN A 496 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117453 restraints weight = 5577.714| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.64 r_work: 0.3110 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4520 Z= 0.149 Angle : 0.528 8.451 6172 Z= 0.271 Chirality : 0.041 0.127 697 Planarity : 0.004 0.032 748 Dihedral : 5.128 77.585 595 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.26 % Allowed : 18.26 % Favored : 78.48 % 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 (0.35), residues: 551 helix: 1.61 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.20 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.022 0.001 TYR A 219 PHE 0.013 0.001 PHE A 691 TRP 0.011 0.001 TRP A 728 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 4520) covalent geometry : angle 0.52787 / 0.27 ( 6172) hydrogen bonds : bond 0.03880 / 2.53 ( 289) hydrogen bonds : angle 4.25560 / 2.86 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.173 Fit side-chains REVERT: A 219 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.6105 (p90) REVERT: A 398 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8245 (tp) REVERT: A 430 TYR cc_start: 0.8003 (m-80) cc_final: 0.7594 (m-80) REVERT: A 431 VAL cc_start: 0.8627 (p) cc_final: 0.8273 (m) REVERT: A 492 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8214 (t0) REVERT: A 584 GLU cc_start: 0.8368 (tp30) cc_final: 0.7994 (tp30) outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.0473 time to fit residues: 6.6174 Evaluate side-chains 102 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 30 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118959 restraints weight = 5550.999| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.63 r_work: 0.3231 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4520 Z= 0.124 Angle : 0.520 8.572 6172 Z= 0.265 Chirality : 0.041 0.126 697 Planarity : 0.004 0.032 748 Dihedral : 5.081 76.202 595 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.04 % Allowed : 18.26 % Favored : 78.70 % 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: 1.65 (0.36), residues: 551 helix: 1.65 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.17 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.021 0.001 TYR A 219 PHE 0.014 0.001 PHE A 629 TRP 0.009 0.001 TRP A 728 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 4520) covalent geometry : angle 0.51973 / 0.27 ( 6172) hydrogen bonds : bond 0.03753 / 2.47 ( 289) hydrogen bonds : angle 4.20494 / 2.83 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.157 Fit side-chains REVERT: A 219 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.6033 (p90) REVERT: A 398 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (tp) REVERT: A 431 VAL cc_start: 0.8684 (p) cc_final: 0.8327 (m) REVERT: A 584 GLU cc_start: 0.8334 (tp30) cc_final: 0.7995 (tp30) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0492 time to fit residues: 6.6694 Evaluate side-chains 97 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 38 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 14 optimal weight: 0.0010 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.0020 chunk 32 optimal weight: 0.7980 overall best weight: 0.0508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.143710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127153 restraints weight = 5578.472| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.57 r_work: 0.3305 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4520 Z= 0.104 Angle : 0.505 8.865 6172 Z= 0.256 Chirality : 0.040 0.122 697 Planarity : 0.004 0.032 748 Dihedral : 4.831 72.275 595 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.52 % Allowed : 18.91 % Favored : 79.57 % 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: 1.82 (0.36), residues: 551 helix: 1.75 (0.26), residues: 395 sheet: None (None), residues: 0 loop : -0.12 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.017 0.001 TYR A 219 PHE 0.015 0.001 PHE A 691 TRP 0.009 0.001 TRP A 713 HIS 0.000 0.000 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 4520) covalent geometry : angle 0.50511 / 0.26 ( 6172) hydrogen bonds : bond 0.03316 / 2.22 ( 289) hydrogen bonds : angle 3.97780 / 2.69 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.153 Fit side-chains REVERT: A 219 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.5890 (p90) REVERT: A 431 VAL cc_start: 0.8593 (p) cc_final: 0.8271 (m) REVERT: A 559 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 584 GLU cc_start: 0.8203 (tp30) cc_final: 0.7847 (tp30) outliers start: 7 outliers final: 1 residues processed: 108 average time/residue: 0.0460 time to fit residues: 7.1171 Evaluate side-chains 96 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.134796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117567 restraints weight = 5652.487| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.60 r_work: 0.3028 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4520 Z= 0.148 Angle : 0.560 8.761 6172 Z= 0.287 Chirality : 0.042 0.141 697 Planarity : 0.004 0.031 748 Dihedral : 4.941 71.498 595 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.65 % Allowed : 20.43 % Favored : 78.91 % 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: 1.64 (0.36), residues: 551 helix: 1.66 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.29 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.022 0.001 TYR A 219 PHE 0.020 0.001 PHE A 691 TRP 0.013 0.001 TRP A 467 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 4520) covalent geometry : angle 0.56017 / 0.29 ( 6172) hydrogen bonds : bond 0.03782 / 2.43 ( 289) hydrogen bonds : angle 4.14500 / 2.79 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.164 Fit side-chains REVERT: A 219 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.6179 (p90) REVERT: A 431 VAL cc_start: 0.8594 (p) cc_final: 0.8275 (m) REVERT: A 584 GLU cc_start: 0.8336 (tp30) cc_final: 0.7978 (tp30) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.0459 time to fit residues: 5.8487 Evaluate side-chains 87 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 ASN ** 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 = 0.3600 r_free = 0.3600 target = 0.138017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120647 restraints weight = 5602.272| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.65 r_work: 0.3022 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4520 Z= 0.132 Angle : 0.552 8.859 6172 Z= 0.282 Chirality : 0.042 0.137 697 Planarity : 0.004 0.031 748 Dihedral : 4.795 63.812 595 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.65 % Allowed : 20.43 % Favored : 78.91 % 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: 1.62 (0.36), residues: 551 helix: 1.64 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -0.30 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.021 0.001 TYR A 207 PHE 0.020 0.001 PHE A 691 TRP 0.013 0.001 TRP A 467 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 4520) covalent geometry : angle 0.55155 / 0.28 ( 6172) hydrogen bonds : bond 0.03744 / 2.43 ( 289) hydrogen bonds : angle 4.14469 / 2.78 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1258.68 seconds wall clock time: 22 minutes 17.94 seconds (1337.94 seconds total)