Starting phenix.real_space_refine on Thu Mar 6 08:44:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvw_37874/03_2025/8wvw_37874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvw_37874/03_2025/8wvw_37874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvw_37874/03_2025/8wvw_37874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvw_37874/03_2025/8wvw_37874.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvw_37874/03_2025/8wvw_37874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvw_37874/03_2025/8wvw_37874.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3634 2.51 5 N 920 2.21 5 O 1014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5594 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5594 Classifications: {'peptide': 722} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 36, 'TRANS': 685} Chain breaks: 6 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.42, per 1000 atoms: 0.79 Number of scatterers: 5594 At special positions: 0 Unit cell: (97.75, 79.05, 147.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1014 8.00 N 920 7.00 C 3634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=1.98 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=1.96 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.06 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.06 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: 1.37 Conformation dependent library (CDL) restraints added in 817.2 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 32.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.525A pdb=" N LYS A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 407 through 411 removed outlier: 4.340A pdb=" N THR A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.912A pdb=" N ALA A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 474 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 564 removed outlier: 3.922A pdb=" N ASN A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 601 removed outlier: 3.621A pdb=" N ASN A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 removed outlier: 4.110A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.661A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.892A pdb=" N ALA A 647 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 666 through 679 removed outlier: 3.832A pdb=" N PHE A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 730 Processing helix chain 'A' and resid 741 through 768 removed outlier: 3.792A pdb=" N CYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) Proline residue: A 762 - end of helix removed outlier: 3.729A pdb=" N PHE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.623A pdb=" N ILE A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 792 through 804 removed outlier: 3.661A pdb=" N LEU A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.785A pdb=" N VAL A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 815 removed outlier: 4.168A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.344A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 62 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 111 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 110 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 159 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 207 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.740A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.281A pdb=" N LEU A 324 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA6, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.909A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 418 " --> pdb=" O LYS A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 147 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 990 1.28 - 1.42: 1335 1.42 - 1.55: 3360 1.55 - 1.69: 2 1.69 - 1.82: 34 Bond restraints: 5721 Sorted by residual: bond pdb=" C TYR A 234 " pdb=" N ASN A 235 " ideal model delta sigma weight residual 1.328 1.466 -0.138 8.50e-03 1.38e+04 2.63e+02 bond pdb=" C THR A 698 " pdb=" N GLY A 699 " ideal model delta sigma weight residual 1.329 1.497 -0.168 1.40e-02 5.10e+03 1.44e+02 bond pdb=" C LEU A 400 " pdb=" N ILE A 401 " ideal model delta sigma weight residual 1.331 1.462 -0.130 1.11e-02 8.12e+03 1.37e+02 bond pdb=" C SER A 94 " pdb=" N PHE A 95 " ideal model delta sigma weight residual 1.331 1.496 -0.165 1.43e-02 4.89e+03 1.33e+02 bond pdb=" C GLY A 432 " pdb=" N LEU A 433 " ideal model delta sigma weight residual 1.330 1.493 -0.163 1.52e-02 4.33e+03 1.15e+02 ... (remaining 5716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 7316 4.03 - 8.05: 421 8.05 - 12.08: 31 12.08 - 16.10: 8 16.10 - 20.13: 2 Bond angle restraints: 7778 Sorted by residual: angle pdb=" N TRP A 474 " pdb=" CA TRP A 474 " pdb=" C TRP A 474 " ideal model delta sigma weight residual 112.58 132.71 -20.13 1.22e+00 6.72e-01 2.72e+02 angle pdb=" N CYS A 532 " pdb=" CA CYS A 532 " pdb=" CB CYS A 532 " ideal model delta sigma weight residual 110.73 93.96 16.77 1.55e+00 4.16e-01 1.17e+02 angle pdb=" C PRO A 531 " pdb=" CA PRO A 531 " pdb=" CB PRO A 531 " ideal model delta sigma weight residual 111.46 97.63 13.83 1.29e+00 6.01e-01 1.15e+02 angle pdb=" C ASN A 805 " pdb=" CA ASN A 805 " pdb=" CB ASN A 805 " ideal model delta sigma weight residual 109.65 96.32 13.33 1.30e+00 5.92e-01 1.05e+02 angle pdb=" O PRO A 697 " pdb=" C PRO A 697 " pdb=" N THR A 698 " ideal model delta sigma weight residual 122.23 133.18 -10.95 1.20e+00 6.94e-01 8.32e+01 ... (remaining 7773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 2807 16.39 - 32.78: 443 32.78 - 49.17: 129 49.17 - 65.56: 21 65.56 - 81.94: 9 Dihedral angle restraints: 3409 sinusoidal: 1317 harmonic: 2092 Sorted by residual: dihedral pdb=" N TRP A 474 " pdb=" C TRP A 474 " pdb=" CA TRP A 474 " pdb=" CB TRP A 474 " ideal model delta harmonic sigma weight residual 122.80 142.90 -20.10 0 2.50e+00 1.60e-01 6.47e+01 dihedral pdb=" C TRP A 474 " pdb=" N TRP A 474 " pdb=" CA TRP A 474 " pdb=" CB TRP A 474 " ideal model delta harmonic sigma weight residual -122.60 -141.75 19.15 0 2.50e+00 1.60e-01 5.87e+01 dihedral pdb=" N CYS A 532 " pdb=" C CYS A 532 " pdb=" CA CYS A 532 " pdb=" CB CYS A 532 " ideal model delta harmonic sigma weight residual 122.80 103.74 19.06 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 3406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 903 0.206 - 0.411: 19 0.411 - 0.617: 0 0.617 - 0.823: 0 0.823 - 1.029: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" CA TRP A 474 " pdb=" N TRP A 474 " pdb=" C TRP A 474 " pdb=" CB TRP A 474 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA SER A 538 " pdb=" N SER A 538 " pdb=" C SER A 538 " pdb=" CB SER A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE A 473 " pdb=" N PHE A 473 " pdb=" C PHE A 473 " pdb=" CB PHE A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 920 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 680 " 0.022 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PRO A 680 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO A 680 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 681 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 541 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C ILE A 541 " -0.067 2.00e-02 2.50e+03 pdb=" O ILE A 541 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG A 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 526 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C THR A 526 " 0.067 2.00e-02 2.50e+03 pdb=" O THR A 526 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY A 527 " -0.023 2.00e-02 2.50e+03 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 240 2.68 - 3.23: 5142 3.23 - 3.79: 8174 3.79 - 4.34: 10645 4.34 - 4.90: 17524 Nonbonded interactions: 41725 Sorted by model distance: nonbonded pdb=" OD1 ASN A 67 " pdb=" ND2 ASN A 91 " model vdw 2.124 3.120 nonbonded pdb=" O THR A 523 " pdb=" C PRO A 524 " model vdw 2.229 3.270 nonbonded pdb=" OE1 GLU A 146 " pdb=" ND1 HIS A 171 " model vdw 2.303 3.120 nonbonded pdb=" O THR A 523 " pdb=" N SER A 525 " model vdw 2.333 3.120 nonbonded pdb=" O SER A 463 " pdb=" OG SER A 463 " model vdw 2.346 3.040 ... (remaining 41720 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 group one per residue 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: 2.920 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.019 0.168 5721 Z= 1.308 Angle : 1.910 20.130 7778 Z= 1.338 Chirality : 0.078 1.029 923 Planarity : 0.010 0.088 982 Dihedral : 17.268 81.943 2028 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.90 % Favored : 90.96 % Rotamer: Outliers : 3.34 % Allowed : 26.11 % Favored : 70.54 % Cbeta Deviations : 1.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.30), residues: 708 helix: -1.45 (0.32), residues: 222 sheet: -2.83 (0.54), residues: 96 loop : -2.32 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 812 HIS 0.010 0.001 HIS A 293 PHE 0.031 0.002 PHE A 547 TYR 0.033 0.003 TYR A 468 ARG 0.003 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.7693 (mmm) cc_final: 0.7400 (mmt) REVERT: A 99 LYS cc_start: 0.7570 (ttpt) cc_final: 0.6928 (tptt) REVERT: A 212 LYS cc_start: 0.7525 (tmtt) cc_final: 0.7075 (tptp) REVERT: A 289 ASN cc_start: 0.7871 (p0) cc_final: 0.7644 (p0) REVERT: A 344 MET cc_start: 0.7636 (mtt) cc_final: 0.7358 (mtm) outliers start: 21 outliers final: 7 residues processed: 107 average time/residue: 0.1413 time to fit residues: 20.7958 Evaluate side-chains 69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 340 GLN A 386 GLN A 458 ASN A 658 HIS A 683 HIS A 797 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.167251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132021 restraints weight = 7278.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132802 restraints weight = 5858.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133909 restraints weight = 4585.768| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5721 Z= 0.229 Angle : 0.673 7.020 7778 Z= 0.339 Chirality : 0.045 0.134 923 Planarity : 0.005 0.048 982 Dihedral : 5.355 55.809 755 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.03 % Allowed : 23.25 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.30), residues: 708 helix: -0.04 (0.36), residues: 213 sheet: -2.81 (0.60), residues: 75 loop : -2.14 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.007 0.002 HIS A 293 PHE 0.019 0.001 PHE A 696 TYR 0.015 0.002 TYR A 725 ARG 0.005 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.556 Fit side-chains REVERT: A 99 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7187 (tptt) REVERT: A 105 LYS cc_start: 0.7897 (ptpp) cc_final: 0.7582 (mtmm) REVERT: A 132 GLN cc_start: 0.7931 (mt0) cc_final: 0.7590 (mt0) REVERT: A 788 ILE cc_start: 0.8361 (tt) cc_final: 0.8152 (tt) outliers start: 19 outliers final: 8 residues processed: 90 average time/residue: 0.1279 time to fit residues: 16.4583 Evaluate side-chains 67 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 175 ASN A 258 ASN A 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.159421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125618 restraints weight = 7221.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.124022 restraints weight = 6166.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.124881 restraints weight = 5524.507| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5721 Z= 0.296 Angle : 0.677 7.716 7778 Z= 0.341 Chirality : 0.046 0.179 923 Planarity : 0.004 0.035 982 Dihedral : 5.134 49.100 750 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.98 % Allowed : 22.77 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.30), residues: 708 helix: -0.05 (0.36), residues: 225 sheet: -3.23 (0.52), residues: 83 loop : -2.10 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 159 HIS 0.006 0.001 HIS A 293 PHE 0.015 0.002 PHE A 385 TYR 0.013 0.002 TYR A 725 ARG 0.005 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.556 Fit side-chains REVERT: A 48 LEU cc_start: 0.4853 (OUTLIER) cc_final: 0.4518 (mt) REVERT: A 66 MET cc_start: 0.7689 (mmm) cc_final: 0.7363 (mmt) REVERT: A 74 GLU cc_start: 0.7374 (pm20) cc_final: 0.6724 (pp20) REVERT: A 105 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7627 (mtmm) REVERT: A 132 GLN cc_start: 0.8252 (mt0) cc_final: 0.8013 (mt0) REVERT: A 517 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: A 712 LEU cc_start: 0.8296 (tt) cc_final: 0.7944 (mt) REVERT: A 752 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8493 (mp) outliers start: 25 outliers final: 15 residues processed: 88 average time/residue: 0.1127 time to fit residues: 14.7223 Evaluate side-chains 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 175 ASN A 258 ASN A 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.156792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.122912 restraints weight = 7368.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.120925 restraints weight = 6399.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122078 restraints weight = 5814.146| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5721 Z= 0.272 Angle : 0.664 10.779 7778 Z= 0.328 Chirality : 0.045 0.168 923 Planarity : 0.004 0.033 982 Dihedral : 4.838 37.359 749 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.34 % Allowed : 22.61 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.30), residues: 708 helix: 0.20 (0.36), residues: 219 sheet: -3.25 (0.53), residues: 73 loop : -2.07 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.007 0.001 HIS A 256 PHE 0.013 0.001 PHE A 808 TYR 0.015 0.002 TYR A 725 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.573 Fit side-chains REVERT: A 48 LEU cc_start: 0.4790 (OUTLIER) cc_final: 0.4372 (mt) REVERT: A 74 GLU cc_start: 0.7160 (pm20) cc_final: 0.6693 (pp20) REVERT: A 105 LYS cc_start: 0.7933 (ptpp) cc_final: 0.7634 (mtmm) REVERT: A 678 CYS cc_start: 0.8231 (t) cc_final: 0.7745 (t) REVERT: A 712 LEU cc_start: 0.8236 (tt) cc_final: 0.7947 (mt) REVERT: A 752 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8497 (mp) outliers start: 21 outliers final: 15 residues processed: 77 average time/residue: 0.1298 time to fit residues: 14.5886 Evaluate side-chains 72 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 782 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.0020 chunk 16 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 175 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.159937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126222 restraints weight = 7191.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.124301 restraints weight = 6429.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125263 restraints weight = 5791.860| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5721 Z= 0.178 Angle : 0.576 6.020 7778 Z= 0.287 Chirality : 0.043 0.133 923 Planarity : 0.004 0.032 982 Dihedral : 4.013 17.668 745 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.23 % Allowed : 23.41 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.31), residues: 708 helix: 0.59 (0.37), residues: 218 sheet: -3.19 (0.56), residues: 69 loop : -1.97 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.006 0.001 HIS A 293 PHE 0.009 0.001 PHE A 80 TYR 0.014 0.001 TYR A 725 ARG 0.003 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.574 Fit side-chains REVERT: A 66 MET cc_start: 0.7620 (mmm) cc_final: 0.7213 (mmt) REVERT: A 105 LYS cc_start: 0.7943 (ptpp) cc_final: 0.7650 (mtmm) REVERT: A 678 CYS cc_start: 0.8052 (t) cc_final: 0.7618 (t) REVERT: A 721 MET cc_start: 0.7046 (ttm) cc_final: 0.6755 (ttm) REVERT: A 752 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8612 (mp) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 0.1358 time to fit residues: 15.3143 Evaluate side-chains 69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 782 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 175 ASN A 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.154449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.120106 restraints weight = 7175.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118585 restraints weight = 5942.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119355 restraints weight = 5340.347| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5721 Z= 0.284 Angle : 0.661 10.885 7778 Z= 0.325 Chirality : 0.045 0.154 923 Planarity : 0.004 0.033 982 Dihedral : 4.347 19.014 745 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.18 % Allowed : 23.25 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.31), residues: 708 helix: 0.48 (0.36), residues: 218 sheet: -3.07 (0.57), residues: 69 loop : -2.04 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS A 293 PHE 0.014 0.001 PHE A 808 TYR 0.014 0.002 TYR A 725 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.613 Fit side-chains REVERT: A 66 MET cc_start: 0.7646 (mmm) cc_final: 0.7313 (mmt) REVERT: A 105 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7727 (mtmm) REVERT: A 250 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8944 (tp) REVERT: A 678 CYS cc_start: 0.8087 (t) cc_final: 0.7798 (t) REVERT: A 752 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 788 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8635 (tt) outliers start: 20 outliers final: 14 residues processed: 75 average time/residue: 0.1248 time to fit residues: 13.7839 Evaluate side-chains 70 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 788 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 175 ASN A 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.155353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121766 restraints weight = 7266.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.119828 restraints weight = 6309.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120910 restraints weight = 5512.457| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5721 Z= 0.307 Angle : 0.661 7.260 7778 Z= 0.332 Chirality : 0.046 0.152 923 Planarity : 0.004 0.034 982 Dihedral : 4.477 21.019 745 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.30 % Allowed : 22.45 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.31), residues: 708 helix: 0.43 (0.36), residues: 217 sheet: -3.17 (0.56), residues: 69 loop : -2.11 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS A 293 PHE 0.014 0.001 PHE A 808 TYR 0.014 0.002 TYR A 725 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.624 Fit side-chains REVERT: A 66 MET cc_start: 0.7629 (mmm) cc_final: 0.7310 (mmt) REVERT: A 105 LYS cc_start: 0.8009 (ptpp) cc_final: 0.7798 (mtmm) REVERT: A 137 ASP cc_start: 0.8606 (p0) cc_final: 0.8360 (p0) REVERT: A 154 GLN cc_start: 0.7059 (tt0) cc_final: 0.6646 (tp-100) REVERT: A 250 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8960 (tp) REVERT: A 712 LEU cc_start: 0.8244 (tt) cc_final: 0.7936 (mt) REVERT: A 752 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 754 PHE cc_start: 0.8050 (t80) cc_final: 0.7593 (t80) outliers start: 27 outliers final: 18 residues processed: 82 average time/residue: 0.1427 time to fit residues: 17.0148 Evaluate side-chains 77 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 781 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 175 ASN A 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.159127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.126200 restraints weight = 7241.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124931 restraints weight = 6101.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125430 restraints weight = 5513.750| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5721 Z= 0.223 Angle : 0.617 11.036 7778 Z= 0.306 Chirality : 0.044 0.194 923 Planarity : 0.004 0.033 982 Dihedral : 4.208 18.049 745 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.71 % Allowed : 22.93 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.31), residues: 708 helix: 0.66 (0.36), residues: 217 sheet: -3.05 (0.56), residues: 69 loop : -2.10 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 812 HIS 0.006 0.001 HIS A 293 PHE 0.010 0.001 PHE A 808 TYR 0.016 0.001 TYR A 725 ARG 0.004 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.628 Fit side-chains REVERT: A 66 MET cc_start: 0.7607 (mmm) cc_final: 0.7293 (mmt) REVERT: A 137 ASP cc_start: 0.8586 (p0) cc_final: 0.8343 (p0) REVERT: A 250 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8953 (tp) REVERT: A 721 MET cc_start: 0.7067 (ttm) cc_final: 0.6743 (ttm) REVERT: A 752 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8634 (mp) outliers start: 17 outliers final: 14 residues processed: 75 average time/residue: 0.1095 time to fit residues: 12.5736 Evaluate side-chains 74 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 781 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 chunk 68 optimal weight: 0.0000 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 258 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.155090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120873 restraints weight = 7257.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.119406 restraints weight = 5734.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120644 restraints weight = 5471.507| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5721 Z= 0.180 Angle : 0.580 9.241 7778 Z= 0.288 Chirality : 0.043 0.198 923 Planarity : 0.003 0.033 982 Dihedral : 3.969 15.730 745 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.39 % Allowed : 24.20 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.31), residues: 708 helix: 0.90 (0.36), residues: 218 sheet: -2.84 (0.64), residues: 53 loop : -2.16 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 812 HIS 0.005 0.001 HIS A 293 PHE 0.010 0.001 PHE A 627 TYR 0.014 0.001 TYR A 725 ARG 0.004 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.565 Fit side-chains REVERT: A 66 MET cc_start: 0.7572 (mmm) cc_final: 0.7262 (mmt) REVERT: A 137 ASP cc_start: 0.8572 (p0) cc_final: 0.8327 (p0) REVERT: A 752 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8561 (mp) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.1024 time to fit residues: 11.5758 Evaluate side-chains 74 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 755 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.0050 chunk 50 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 175 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.157545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121636 restraints weight = 7334.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.121458 restraints weight = 5551.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122338 restraints weight = 4983.772| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5721 Z= 0.170 Angle : 0.591 11.010 7778 Z= 0.288 Chirality : 0.043 0.185 923 Planarity : 0.003 0.032 982 Dihedral : 3.836 14.188 745 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.39 % Allowed : 24.36 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.31), residues: 708 helix: 1.25 (0.37), residues: 211 sheet: -2.93 (0.61), residues: 58 loop : -2.06 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 812 HIS 0.005 0.001 HIS A 293 PHE 0.009 0.001 PHE A 627 TYR 0.014 0.001 TYR A 725 ARG 0.003 0.000 ARG A 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.611 Fit side-chains REVERT: A 66 MET cc_start: 0.7578 (mmm) cc_final: 0.7269 (mmt) REVERT: A 137 ASP cc_start: 0.8522 (p0) cc_final: 0.8278 (p0) REVERT: A 752 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8580 (mp) outliers start: 15 outliers final: 12 residues processed: 73 average time/residue: 0.1155 time to fit residues: 12.8153 Evaluate side-chains 73 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 755 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 171 HIS A 175 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.117848 restraints weight = 7332.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.116106 restraints weight = 6091.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.118196 restraints weight = 5749.370| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5721 Z= 0.305 Angle : 0.664 9.685 7778 Z= 0.328 Chirality : 0.046 0.192 923 Planarity : 0.004 0.035 982 Dihedral : 4.279 18.869 745 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.71 % Allowed : 24.20 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.31), residues: 708 helix: 0.48 (0.36), residues: 219 sheet: -2.58 (0.55), residues: 76 loop : -2.15 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 812 HIS 0.006 0.001 HIS A 293 PHE 0.014 0.001 PHE A 808 TYR 0.016 0.002 TYR A 801 ARG 0.003 0.000 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.24 seconds wall clock time: 34 minutes 59.35 seconds (2099.35 seconds total)