Starting phenix.real_space_refine on Tue Mar 3 12:54:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hug_52411/03_2026/9hug_52411.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hug_52411/03_2026/9hug_52411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hug_52411/03_2026/9hug_52411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hug_52411/03_2026/9hug_52411.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hug_52411/03_2026/9hug_52411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hug_52411/03_2026/9hug_52411.map" } resolution = 2.97 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: 5 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 C 3037 2.51 5 N 675 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4491 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4434 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 31, 'TRANS': 526} Chain breaks: 1 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' CL': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N LYS A 416 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 416 " occ=0.00 residue: pdb=" N THR A 417 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 417 " occ=0.00 residue: pdb=" N SER A 418 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 418 " occ=0.00 residue: pdb=" N GLY A 419 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 419 " occ=0.00 residue: pdb=" N LYS A 420 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 420 " occ=0.00 Time building chain proxies: 1.02, per 1000 atoms: 0.23 Number of scatterers: 4491 At special positions: 0 Unit cell: (85.176, 64.792, 90.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 33 16.00 O 745 8.00 N 675 7.00 C 3037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " 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: 0.34 Conformation dependent library (CDL) restraints added in 337.8 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 1 sheets defined 80.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.572A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Proline residue: A 232 - end of helix removed outlier: 3.757A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.724A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 302 removed outlier: 3.555A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.169A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 393 through 414 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.638A 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 478 removed outlier: 3.951A pdb=" N TRP A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.906A 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 534 through 538 removed outlier: 3.598A pdb=" N VAL A 538 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 559 through 592 removed outlier: 3.792A pdb=" N TRP A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 601 through 616 Processing helix chain 'A' and resid 617 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 636 removed outlier: 3.551A pdb=" N MET A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 655 removed outlier: 3.633A pdb=" N VAL A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 removed outlier: 3.957A pdb=" N MET A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) 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: 3.994A 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 762 through 766 Processing sheet with id=AA1, first strand: chain 'A' and resid 704 through 705 292 hydrogen bonds defined for protein. 837 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: 0.66 Time building geometry restraints manager: 0.48 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: 1279 1.34 - 1.46: 996 1.46 - 1.58: 2313 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4639 Sorted by residual: bond pdb=" CA TRP A 263 " pdb=" C TRP A 263 " ideal model delta sigma weight residual 1.523 1.505 0.019 1.80e-02 3.09e+03 1.06e+00 bond pdb=" CB ILE A 231 " pdb=" CG1 ILE A 231 " ideal model delta sigma weight residual 1.530 1.549 -0.019 2.00e-02 2.50e+03 9.24e-01 bond pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " ideal model delta sigma weight residual 1.532 1.546 -0.013 1.43e-02 4.89e+03 8.91e-01 bond pdb=" CA THR A 462 " pdb=" CB THR A 462 " ideal model delta sigma weight residual 1.530 1.547 -0.016 1.75e-02 3.27e+03 8.45e-01 bond pdb=" N ASP A 757 " pdb=" CA ASP A 757 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.32e-02 5.74e+03 6.80e-01 ... (remaining 4634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 6039 1.51 - 3.01: 248 3.01 - 4.52: 36 4.52 - 6.03: 12 6.03 - 7.53: 3 Bond angle restraints: 6338 Sorted by residual: angle pdb=" C LEU A 559 " pdb=" N SER A 560 " pdb=" CA SER A 560 " ideal model delta sigma weight residual 120.06 124.96 -4.90 1.19e+00 7.06e-01 1.70e+01 angle pdb=" CB ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CD1 ILE A 231 " ideal model delta sigma weight residual 113.80 120.05 -6.25 2.10e+00 2.27e-01 8.86e+00 angle pdb=" CA TYR A 286 " pdb=" CB TYR A 286 " pdb=" CG TYR A 286 " ideal model delta sigma weight residual 113.90 119.10 -5.20 1.80e+00 3.09e-01 8.36e+00 angle pdb=" CA TYR A 287 " pdb=" CB TYR A 287 " pdb=" CG TYR A 287 " ideal model delta sigma weight residual 113.90 118.89 -4.99 1.80e+00 3.09e-01 7.69e+00 angle pdb=" CA TRP A 482 " pdb=" CB TRP A 482 " pdb=" CG TRP A 482 " ideal model delta sigma weight residual 113.60 118.56 -4.96 1.90e+00 2.77e-01 6.83e+00 ... (remaining 6333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2535 17.92 - 35.85: 170 35.85 - 53.77: 29 53.77 - 71.70: 6 71.70 - 89.62: 5 Dihedral angle restraints: 2745 sinusoidal: 1129 harmonic: 1616 Sorted by residual: dihedral pdb=" CA GLN A 755 " pdb=" C GLN A 755 " pdb=" N PRO A 756 " pdb=" CA PRO A 756 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+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 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASP A 540 " pdb=" C ASP A 540 " pdb=" N GLN A 541 " pdb=" CA GLN A 541 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 489 0.043 - 0.086: 177 0.086 - 0.129: 42 0.129 - 0.173: 9 0.173 - 0.216: 1 Chirality restraints: 718 Sorted by residual: chirality pdb=" CA ASP A 757 " pdb=" N ASP A 757 " pdb=" C ASP A 757 " pdb=" CB ASP A 757 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PRO A 429 " pdb=" N PRO A 429 " pdb=" C PRO A 429 " pdb=" CB PRO A 429 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA TRP A 482 " pdb=" N TRP A 482 " pdb=" C TRP A 482 " pdb=" CB TRP A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 715 not shown) Planarity restraints: 756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 290 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE A 290 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE A 290 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 291 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 279 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ILE A 279 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE A 279 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 280 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 502 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR A 502 " -0.056 2.00e-02 2.50e+03 pdb=" O THR A 502 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A 503 " 0.019 2.00e-02 2.50e+03 ... (remaining 753 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1717 2.89 - 3.40: 4782 3.40 - 3.90: 7693 3.90 - 4.40: 9114 4.40 - 4.90: 15086 Nonbonded interactions: 38392 Sorted by model distance: nonbonded pdb=" OH TYR A 656 " pdb=" OD2 ASP A 664 " model vdw 2.392 3.040 nonbonded pdb=" OG SER A 371 " pdb=" OE1 GLU A 552 " model vdw 2.403 3.040 nonbonded pdb=" OG1 THR A 317 " pdb=" OE2 GLU A 373 " model vdw 2.445 3.040 nonbonded pdb=" OG SER A 383 " pdb=" O TYR A 388 " model vdw 2.472 3.040 nonbonded pdb=" OE1 GLU A 387 " pdb=" OH TYR A 708 " model vdw 2.478 3.040 ... (remaining 38387 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=0.00 max=1.00 mean=0.99 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: 2.610 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: 0.100 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.750 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4640 Z= 0.161 Angle : 0.727 7.532 6340 Z= 0.430 Chirality : 0.047 0.216 718 Planarity : 0.007 0.033 756 Dihedral : 12.911 89.621 1710 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.42 % Allowed : 4.83 % Favored : 94.75 % 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: -1.25 (0.31), residues: 554 helix: -0.83 (0.23), residues: 376 sheet: None (None), residues: 0 loop : -0.40 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 769 TYR 0.032 0.005 TYR A 287 PHE 0.017 0.001 PHE A 521 TRP 0.030 0.002 TRP A 482 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4639) covalent geometry : angle 0.72677 ( 6338) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.33244 ( 2) hydrogen bonds : bond 0.14361 ( 292) hydrogen bonds : angle 7.19063 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.158 Fit side-chains REVERT: A 441 VAL cc_start: 0.7958 (t) cc_final: 0.7658 (m) REVERT: A 712 ASN cc_start: 0.7883 (m-40) cc_final: 0.7452 (m110) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.4648 time to fit residues: 27.8030 Evaluate side-chains 48 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 288 ASN A 765 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107162 restraints weight = 5103.044| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.85 r_work: 0.3082 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4640 Z= 0.129 Angle : 0.553 5.745 6340 Z= 0.289 Chirality : 0.043 0.182 718 Planarity : 0.005 0.037 756 Dihedral : 5.396 27.285 729 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.63 % Allowed : 7.56 % Favored : 91.81 % 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: 1.25 (0.36), residues: 554 helix: 1.31 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.023 0.002 TYR A 286 PHE 0.012 0.001 PHE A 521 TRP 0.023 0.001 TRP A 482 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4639) covalent geometry : angle 0.55336 ( 6338) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.64032 ( 2) hydrogen bonds : bond 0.04198 ( 292) hydrogen bonds : angle 4.85763 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.179 Fit side-chains REVERT: A 223 GLN cc_start: 0.8219 (tt0) cc_final: 0.7966 (tt0) REVERT: A 712 ASN cc_start: 0.7730 (m-40) cc_final: 0.7339 (m110) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.4405 time to fit residues: 27.2362 Evaluate side-chains 51 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.127103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102306 restraints weight = 5074.585| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.83 r_work: 0.3028 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4640 Z= 0.154 Angle : 0.557 5.841 6340 Z= 0.288 Chirality : 0.044 0.170 718 Planarity : 0.005 0.040 756 Dihedral : 5.277 28.504 727 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.68 % Allowed : 8.40 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.37), residues: 554 helix: 1.56 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.11 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.023 0.002 TYR A 286 PHE 0.011 0.001 PHE A 521 TRP 0.022 0.001 TRP A 482 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4639) covalent geometry : angle 0.55694 ( 6338) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.62190 ( 2) hydrogen bonds : bond 0.04362 ( 292) hydrogen bonds : angle 4.60167 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.135 Fit side-chains REVERT: A 223 GLN cc_start: 0.8362 (tt0) cc_final: 0.8140 (tt0) REVERT: A 577 ASP cc_start: 0.7331 (p0) cc_final: 0.6863 (m-30) REVERT: A 712 ASN cc_start: 0.7798 (m-40) cc_final: 0.7404 (m110) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.4423 time to fit residues: 24.1490 Evaluate side-chains 51 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 726 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.129093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104548 restraints weight = 5055.126| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.78 r_work: 0.3046 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4640 Z= 0.146 Angle : 0.535 5.721 6340 Z= 0.275 Chirality : 0.043 0.174 718 Planarity : 0.005 0.040 756 Dihedral : 5.218 32.433 727 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.47 % Allowed : 9.45 % Favored : 89.08 % 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: 1.71 (0.37), residues: 554 helix: 1.68 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.02 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.021 0.002 TYR A 286 PHE 0.011 0.001 PHE A 521 TRP 0.020 0.001 TRP A 482 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4639) covalent geometry : angle 0.53484 ( 6338) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.57417 ( 2) hydrogen bonds : bond 0.04178 ( 292) hydrogen bonds : angle 4.45317 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.142 Fit side-chains REVERT: A 223 GLN cc_start: 0.8300 (tt0) cc_final: 0.8098 (tt0) REVERT: A 577 ASP cc_start: 0.7190 (p0) cc_final: 0.6846 (m-30) REVERT: A 712 ASN cc_start: 0.7752 (m-40) cc_final: 0.7365 (m110) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.4533 time to fit residues: 25.7222 Evaluate side-chains 54 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 726 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.131997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107137 restraints weight = 5099.185| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.85 r_work: 0.3080 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4640 Z= 0.112 Angle : 0.495 5.977 6340 Z= 0.253 Chirality : 0.041 0.161 718 Planarity : 0.004 0.036 756 Dihedral : 5.025 35.615 727 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.47 % Allowed : 10.08 % Favored : 88.45 % 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: 2.08 (0.37), residues: 554 helix: 2.01 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.01 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 769 TYR 0.019 0.001 TYR A 287 PHE 0.012 0.001 PHE A 580 TRP 0.017 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4639) covalent geometry : angle 0.49496 ( 6338) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.43913 ( 2) hydrogen bonds : bond 0.03664 ( 292) hydrogen bonds : angle 4.25107 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.163 Fit side-chains REVERT: A 712 ASN cc_start: 0.7766 (m-40) cc_final: 0.7400 (m110) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.5213 time to fit residues: 29.4511 Evaluate side-chains 51 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 726 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.130894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105968 restraints weight = 5229.555| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.88 r_work: 0.3060 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4640 Z= 0.127 Angle : 0.514 6.459 6340 Z= 0.261 Chirality : 0.042 0.158 718 Planarity : 0.004 0.036 756 Dihedral : 5.024 36.671 727 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.47 % Allowed : 10.92 % Favored : 87.61 % 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: 2.12 (0.37), residues: 554 helix: 2.08 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.07 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 769 TYR 0.021 0.002 TYR A 286 PHE 0.014 0.001 PHE A 580 TRP 0.017 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4639) covalent geometry : angle 0.51366 ( 6338) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.46138 ( 2) hydrogen bonds : bond 0.03826 ( 292) hydrogen bonds : angle 4.25402 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.164 Fit side-chains REVERT: A 712 ASN cc_start: 0.7810 (m-40) cc_final: 0.7422 (m110) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.4639 time to fit residues: 24.4026 Evaluate side-chains 46 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 707 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 0.0570 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.134079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109336 restraints weight = 5125.150| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.87 r_work: 0.3109 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4640 Z= 0.102 Angle : 0.482 6.913 6340 Z= 0.245 Chirality : 0.040 0.154 718 Planarity : 0.004 0.035 756 Dihedral : 4.874 39.442 727 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.63 % Allowed : 11.97 % Favored : 87.39 % 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: 2.37 (0.37), residues: 554 helix: 2.31 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.07 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 766 TYR 0.021 0.001 TYR A 286 PHE 0.013 0.001 PHE A 580 TRP 0.015 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 4639) covalent geometry : angle 0.48225 ( 6338) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.39719 ( 2) hydrogen bonds : bond 0.03406 ( 292) hydrogen bonds : angle 4.11024 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.162 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.4923 time to fit residues: 24.7782 Evaluate side-chains 47 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 707 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.131085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106221 restraints weight = 5187.805| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.87 r_work: 0.3060 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4640 Z= 0.133 Angle : 0.514 7.558 6340 Z= 0.261 Chirality : 0.042 0.153 718 Planarity : 0.004 0.037 756 Dihedral : 4.981 39.203 727 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.05 % Allowed : 11.97 % Favored : 86.97 % 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: 2.16 (0.37), residues: 554 helix: 2.09 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.07 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 531 TYR 0.021 0.002 TYR A 286 PHE 0.011 0.001 PHE A 580 TRP 0.017 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4639) covalent geometry : angle 0.51383 ( 6338) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.52646 ( 2) hydrogen bonds : bond 0.03856 ( 292) hydrogen bonds : angle 4.24230 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.132 Fit side-chains REVERT: A 712 ASN cc_start: 0.7825 (m-40) cc_final: 0.7418 (m110) outliers start: 5 outliers final: 5 residues processed: 50 average time/residue: 0.4523 time to fit residues: 23.6640 Evaluate side-chains 51 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 726 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105226 restraints weight = 5170.603| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.87 r_work: 0.3047 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4640 Z= 0.140 Angle : 0.531 9.999 6340 Z= 0.269 Chirality : 0.042 0.154 718 Planarity : 0.004 0.037 756 Dihedral : 5.051 40.203 727 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.26 % Allowed : 12.18 % Favored : 86.55 % 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: 2.07 (0.37), residues: 554 helix: 2.02 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.11 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.023 0.002 TYR A 287 PHE 0.012 0.001 PHE A 580 TRP 0.017 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4639) covalent geometry : angle 0.53060 ( 6338) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.55252 ( 2) hydrogen bonds : bond 0.03957 ( 292) hydrogen bonds : angle 4.29626 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.125 Fit side-chains REVERT: A 712 ASN cc_start: 0.7822 (m-40) cc_final: 0.7422 (m110) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.4633 time to fit residues: 24.3301 Evaluate side-chains 52 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 726 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.131160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106341 restraints weight = 5095.045| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.85 r_work: 0.3066 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4640 Z= 0.127 Angle : 0.526 12.858 6340 Z= 0.262 Chirality : 0.041 0.153 718 Planarity : 0.004 0.036 756 Dihedral : 5.022 42.134 727 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.26 % Allowed : 12.39 % Favored : 86.34 % 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: 2.17 (0.37), residues: 554 helix: 2.10 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.08 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 531 TYR 0.024 0.002 TYR A 287 PHE 0.014 0.001 PHE A 580 TRP 0.016 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4639) covalent geometry : angle 0.52566 ( 6338) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.49127 ( 2) hydrogen bonds : bond 0.03795 ( 292) hydrogen bonds : angle 4.26142 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.139 Fit side-chains REVERT: A 712 ASN cc_start: 0.7809 (m-40) cc_final: 0.7420 (m110) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.4751 time to fit residues: 25.4019 Evaluate side-chains 51 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 726 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.133423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108375 restraints weight = 5134.219| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.83 r_work: 0.3102 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4640 Z= 0.119 Angle : 0.509 11.137 6340 Z= 0.255 Chirality : 0.041 0.167 718 Planarity : 0.004 0.036 756 Dihedral : 5.001 44.348 727 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.84 % Allowed : 12.61 % Favored : 86.55 % 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: 2.28 (0.37), residues: 554 helix: 2.20 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 766 TYR 0.019 0.001 TYR A 286 PHE 0.010 0.001 PHE A 521 TRP 0.016 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4639) covalent geometry : angle 0.50888 ( 6338) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.51174 ( 2) hydrogen bonds : bond 0.03677 ( 292) hydrogen bonds : angle 4.23429 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1457.00 seconds wall clock time: 25 minutes 36.49 seconds (1536.49 seconds total)