Starting phenix.real_space_refine on Fri Dec 27 15:12:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvw_37874/12_2024/8wvw_37874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvw_37874/12_2024/8wvw_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_37874/12_2024/8wvw_37874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvw_37874/12_2024/8wvw_37874.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvw_37874/12_2024/8wvw_37874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvw_37874/12_2024/8wvw_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-5532/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: 4.67, per 1000 atoms: 0.83 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: 1.46 Conformation dependent library (CDL) restraints added in 860.8 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: 0.65 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: 1.65 Time building geometry restraints manager: 1.69 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: 1.940 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.490 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- 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 : 0.661 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: 0.1529 time to fit residues: 22.4589 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 : 0.647 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.708 Fit side-chains REVERT: A 99 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7067 (tptt) REVERT: A 105 LYS cc_start: 0.7972 (ptpp) cc_final: 0.7638 (mtmm) REVERT: A 132 GLN cc_start: 0.7899 (mt0) cc_final: 0.7598 (mt0) REVERT: A 589 ILE cc_start: 0.8214 (mm) cc_final: 0.8000 (mt) REVERT: A 788 ILE cc_start: 0.8297 (tt) cc_final: 0.8093 (tt) outliers start: 19 outliers final: 8 residues processed: 90 average time/residue: 0.1373 time to fit residues: 17.8799 Evaluate side-chains 68 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5721 Z= 0.190 Angle : 0.604 5.800 7778 Z= 0.302 Chirality : 0.044 0.166 923 Planarity : 0.004 0.034 982 Dihedral : 4.828 45.586 750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.18 % Allowed : 22.77 % 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: -2.07 (0.31), residues: 708 helix: 0.22 (0.36), residues: 226 sheet: -2.89 (0.59), residues: 76 loop : -2.08 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.007 0.001 HIS A 293 PHE 0.009 0.001 PHE A 808 TYR 0.013 0.001 TYR A 534 ARG 0.003 0.000 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 79 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.647 Fit side-chains REVERT: A 48 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4862 (mt) REVERT: A 66 MET cc_start: 0.7739 (mmm) cc_final: 0.7409 (mmt) REVERT: A 105 LYS cc_start: 0.8073 (ptpp) cc_final: 0.7739 (mtmm) REVERT: A 132 GLN cc_start: 0.8123 (mt0) cc_final: 0.7826 (mt0) REVERT: A 331 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7498 (mt) REVERT: A 589 ILE cc_start: 0.8177 (mm) cc_final: 0.7951 (mt) REVERT: A 752 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 788 ILE cc_start: 0.8470 (tt) cc_final: 0.8270 (tt) outliers start: 20 outliers final: 10 residues processed: 74 average time/residue: 0.1372 time to fit residues: 14.6119 Evaluate side-chains 69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 261 SER Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 664 VAL 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 64 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 18 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3578 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= 0.277 Angle : 0.665 11.134 7778 Z= 0.330 Chirality : 0.045 0.173 923 Planarity : 0.004 0.031 982 Dihedral : 4.431 23.168 746 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.03 % Allowed : 21.97 % Favored : 75.00 % 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: -2.08 (0.30), residues: 708 helix: 0.28 (0.36), residues: 219 sheet: -3.22 (0.54), residues: 74 loop : -2.02 (0.28), residues: 415 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 0.001 PHE A 808 TYR 0.013 0.002 TYR A 725 ARG 0.003 0.000 ARG A 275 *********************** 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 85 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.626 Fit side-chains REVERT: A 48 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4713 (mt) REVERT: A 105 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7728 (mtmm) REVERT: A 331 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7600 (mt) REVERT: A 712 LEU cc_start: 0.8195 (tt) cc_final: 0.7800 (mt) REVERT: A 752 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8360 (mp) outliers start: 19 outliers final: 12 residues processed: 80 average time/residue: 0.1174 time to fit residues: 14.0268 Evaluate side-chains 71 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 331 ILE 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 752 LEU 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 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5721 Z= 0.219 Angle : 0.605 7.285 7778 Z= 0.303 Chirality : 0.044 0.137 923 Planarity : 0.004 0.030 982 Dihedral : 4.127 19.189 745 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.66 % Allowed : 21.82 % Favored : 74.52 % 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: -1.83 (0.31), residues: 708 helix: 0.48 (0.36), residues: 218 sheet: -2.68 (0.55), residues: 85 loop : -1.90 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.006 0.001 HIS A 256 PHE 0.011 0.001 PHE A 808 TYR 0.015 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 83 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.711 Fit side-chains REVERT: A 48 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4614 (mt) REVERT: A 105 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7772 (mtmm) REVERT: A 331 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7574 (mt) REVERT: A 678 CYS cc_start: 0.8181 (t) cc_final: 0.7540 (t) REVERT: A 752 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 788 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (tt) outliers start: 23 outliers final: 16 residues processed: 77 average time/residue: 0.1312 time to fit residues: 14.7166 Evaluate side-chains 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 110 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 227 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 331 ILE 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 Chi-restraints excluded: chain A residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4137 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= 0.293 Angle : 0.659 10.878 7778 Z= 0.326 Chirality : 0.045 0.156 923 Planarity : 0.004 0.033 982 Dihedral : 4.343 19.459 745 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.14 % Allowed : 21.18 % Favored : 74.68 % 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: -1.94 (0.31), residues: 708 helix: 0.39 (0.36), residues: 218 sheet: -2.77 (0.52), residues: 88 loop : -1.95 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.006 0.001 HIS A 293 PHE 0.015 0.001 PHE A 808 TYR 0.014 0.002 TYR A 725 ARG 0.004 0.000 ARG A 275 *********************** 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 84 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.707 Fit side-chains REVERT: A 48 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.4626 (mt) REVERT: A 66 MET cc_start: 0.7739 (mmm) cc_final: 0.7415 (mmt) REVERT: A 105 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7803 (mtmm) REVERT: A 331 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 344 MET cc_start: 0.7972 (mtt) cc_final: 0.7729 (mtm) REVERT: A 678 CYS cc_start: 0.8175 (t) cc_final: 0.7667 (t) REVERT: A 752 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 788 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8481 (tt) outliers start: 26 outliers final: 18 residues processed: 79 average time/residue: 0.1377 time to fit residues: 16.1227 Evaluate side-chains 75 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 110 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 227 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 331 ILE 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 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 7 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5721 Z= 0.235 Angle : 0.604 6.278 7778 Z= 0.305 Chirality : 0.044 0.135 923 Planarity : 0.004 0.032 982 Dihedral : 4.201 18.810 745 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.82 % Allowed : 21.97 % Favored : 74.20 % 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 (0.36), residues: 217 sheet: -2.71 (0.54), residues: 81 loop : -2.02 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.005 0.001 HIS A 293 PHE 0.011 0.001 PHE A 808 TYR 0.014 0.001 TYR A 725 ARG 0.003 0.000 ARG A 275 *********************** 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 81 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.678 Fit side-chains REVERT: A 48 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.4936 (mm) REVERT: A 66 MET cc_start: 0.7700 (mmm) cc_final: 0.7380 (mmt) REVERT: A 105 LYS cc_start: 0.8073 (ptpp) cc_final: 0.7824 (mtmm) REVERT: A 250 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8981 (tp) REVERT: A 331 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7602 (mt) REVERT: A 678 CYS cc_start: 0.8099 (t) cc_final: 0.7736 (t) REVERT: A 752 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 788 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8419 (tt) outliers start: 24 outliers final: 17 residues processed: 76 average time/residue: 0.1217 time to fit residues: 14.0036 Evaluate side-chains 78 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 110 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 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 331 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5721 Z= 0.225 Angle : 0.608 10.893 7778 Z= 0.302 Chirality : 0.044 0.134 923 Planarity : 0.004 0.033 982 Dihedral : 4.116 17.579 745 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.82 % Allowed : 21.82 % 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: -1.82 (0.31), residues: 708 helix: 0.71 (0.36), residues: 217 sheet: -2.72 (0.53), residues: 83 loop : -2.02 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.005 0.001 HIS A 293 PHE 0.011 0.001 PHE A 808 TYR 0.014 0.001 TYR A 725 ARG 0.002 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 83 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.665 Fit side-chains REVERT: A 48 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.4917 (mm) REVERT: A 66 MET cc_start: 0.7709 (mmm) cc_final: 0.7406 (mmt) REVERT: A 331 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 678 CYS cc_start: 0.8018 (t) cc_final: 0.7734 (t) REVERT: A 752 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8446 (mp) outliers start: 24 outliers final: 18 residues processed: 78 average time/residue: 0.1274 time to fit residues: 14.9354 Evaluate side-chains 75 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 110 LEU 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 242 GLN 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 331 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 41 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5721 Z= 0.196 Angle : 0.584 9.171 7778 Z= 0.292 Chirality : 0.044 0.196 923 Planarity : 0.003 0.033 982 Dihedral : 3.986 16.392 745 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.87 % Allowed : 22.61 % Favored : 74.52 % 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: -1.71 (0.31), residues: 708 helix: 1.05 (0.36), residues: 210 sheet: -3.02 (0.60), residues: 59 loop : -2.09 (0.28), residues: 439 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 808 TYR 0.016 0.001 TYR A 725 ARG 0.003 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 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.589 Fit side-chains REVERT: A 66 MET cc_start: 0.7696 (mmm) cc_final: 0.7394 (mmt) REVERT: A 331 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7520 (mt) REVERT: A 678 CYS cc_start: 0.7960 (t) cc_final: 0.7729 (t) REVERT: A 752 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8462 (mp) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.1262 time to fit residues: 14.4039 Evaluate side-chains 74 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 242 GLN Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4562 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= 0.301 Angle : 0.668 11.475 7778 Z= 0.329 Chirality : 0.046 0.193 923 Planarity : 0.004 0.034 982 Dihedral : 4.280 19.010 745 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.34 % Allowed : 22.93 % 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: -1.98 (0.31), residues: 708 helix: 0.44 (0.35), residues: 224 sheet: -2.63 (0.55), residues: 77 loop : -2.16 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.006 0.001 HIS A 293 PHE 0.015 0.001 PHE A 808 TYR 0.015 0.002 TYR A 801 ARG 0.002 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 77 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.645 Fit side-chains REVERT: A 66 MET cc_start: 0.7611 (mmm) cc_final: 0.7316 (mmt) REVERT: A 137 ASP cc_start: 0.8913 (p0) cc_final: 0.8645 (p0) REVERT: A 331 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7617 (mt) REVERT: A 344 MET cc_start: 0.7979 (mtt) cc_final: 0.7741 (mtm) REVERT: A 678 CYS cc_start: 0.8024 (t) cc_final: 0.7808 (t) REVERT: A 752 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8436 (mp) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.1334 time to fit residues: 14.8225 Evaluate side-chains 74 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 242 GLN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 461 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.159380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.126296 restraints weight = 7146.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.124280 restraints weight = 6113.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125326 restraints weight = 5586.549| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5721 Z= 0.228 Angle : 0.609 9.031 7778 Z= 0.303 Chirality : 0.044 0.194 923 Planarity : 0.004 0.034 982 Dihedral : 4.103 17.709 745 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.87 % Allowed : 23.25 % Favored : 73.89 % 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 (0.30), residues: 708 helix: 0.59 (0.36), residues: 223 sheet: -2.78 (0.65), residues: 49 loop : -2.22 (0.28), residues: 436 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 0.011 0.001 PHE A 808 TYR 0.013 0.001 TYR A 725 ARG 0.002 0.000 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1457.32 seconds wall clock time: 27 minutes 15.55 seconds (1635.55 seconds total)