Starting phenix.real_space_refine on Fri Jul 3 04:53:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m5o_23678/07_2026/7m5o_23678.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.173 sd= 0.984 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 261 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 37 5.49 5 S 20 5.16 5 C 3633 2.51 5 N 1104 2.21 5 O 1218 1.98 5 H 5635 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11648 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 10449 Classifications: {'peptide': 655} Link IDs: {'PTRANS': 39, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1198 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 10, 'rna3p': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9735 SG CYS A 667 47.731 13.611 37.310 1.00139.12 S ATOM 9782 SG CYS A 670 48.241 12.976 33.639 1.00137.51 S ATOM 9984 SG CYS A 685 44.845 12.824 35.611 1.00142.82 S ATOM 10024 SG CYS A 688 47.103 9.939 35.540 1.00139.82 S Time building chain proxies: 1.82, per 1000 atoms: 0.16 Number of scatterers: 11648 At special positions: 0 Unit cell: (79.165, 88.085, 111.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 20 16.00 P 37 15.00 O 1218 8.00 N 1104 7.00 C 3633 6.00 H 5635 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 229.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 688 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 670 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 685 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 667 " Number of angles added : 6 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 45.8% alpha, 8.7% beta 5 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.582A pdb=" N ALA A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.912A pdb=" N ARG A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 129 through 169 removed outlier: 3.999A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.650A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.930A pdb=" N ASP A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.994A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 383 removed outlier: 4.085A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.658A pdb=" N GLN A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.613A pdb=" N GLU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 567 removed outlier: 3.965A pdb=" N LEU A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 597 removed outlier: 3.930A pdb=" N LEU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 removed outlier: 3.602A pdb=" N PHE A 626 " --> pdb=" O TRP A 623 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 623 through 627' Processing helix chain 'A' and resid 635 through 651 removed outlier: 4.174A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 removed outlier: 4.612A pdb=" N THR A 663 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 659 through 664' Processing helix chain 'A' and resid 674 through 678 removed outlier: 4.245A pdb=" N ARG A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.863A pdb=" N THR A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.543A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 68 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 304 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.656A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 658 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 604 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 391 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLU A 606 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ILE A 393 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5623 1.04 - 1.23: 113 1.23 - 1.43: 2616 1.43 - 1.63: 3478 1.63 - 1.82: 25 Bond restraints: 11855 Sorted by residual: bond pdb=" CA PRO A 191 " pdb=" C PRO A 191 " ideal model delta sigma weight residual 1.517 1.523 -0.006 6.70e-03 2.23e+04 8.64e-01 bond pdb=" CB LYS A 669 " pdb=" CG LYS A 669 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.57e-01 bond pdb=" CB CYS A 685 " pdb=" HB3 CYS A 685 " ideal model delta sigma weight residual 0.970 0.987 -0.017 2.00e-02 2.50e+03 7.04e-01 bond pdb=" N ILE A 232 " pdb=" CA ILE A 232 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.22e-02 6.72e+03 6.55e-01 bond pdb=" CB TRP A 287 " pdb=" CG TRP A 287 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.39e-01 ... (remaining 11850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 19576 0.99 - 1.98: 1609 1.98 - 2.98: 187 2.98 - 3.97: 44 3.97 - 4.96: 4 Bond angle restraints: 21420 Sorted by residual: angle pdb=" CA CYS A 685 " pdb=" CB CYS A 685 " pdb=" SG CYS A 685 " ideal model delta sigma weight residual 114.40 109.44 4.96 2.30e+00 1.89e-01 4.65e+00 angle pdb=" N ASP A 421 " pdb=" CA ASP A 421 " pdb=" C ASP A 421 " ideal model delta sigma weight residual 108.13 111.72 -3.59 1.72e+00 3.38e-01 4.36e+00 angle pdb=" CA GLU A 632 " pdb=" CB GLU A 632 " pdb=" CG GLU A 632 " ideal model delta sigma weight residual 114.10 118.03 -3.93 2.00e+00 2.50e-01 3.87e+00 angle pdb=" N GLU A 411 " pdb=" CA GLU A 411 " pdb=" C GLU A 411 " ideal model delta sigma weight residual 109.50 106.54 2.96 1.58e+00 4.01e-01 3.52e+00 angle pdb=" N THR A 409 " pdb=" CA THR A 409 " pdb=" C THR A 409 " ideal model delta sigma weight residual 110.80 106.89 3.91 2.13e+00 2.20e-01 3.37e+00 ... (remaining 21415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.17: 5149 26.17 - 52.35: 242 52.35 - 78.52: 56 78.52 - 104.69: 9 104.69 - 130.86: 3 Dihedral angle restraints: 5459 sinusoidal: 3260 harmonic: 2199 Sorted by residual: dihedral pdb=" CA PRO A 660 " pdb=" C PRO A 660 " pdb=" N GLU A 661 " pdb=" CA GLU A 661 " ideal model delta harmonic sigma weight residual -180.00 -148.91 -31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ASP A 421 " pdb=" C ASP A 421 " pdb=" N ARG A 422 " pdb=" CA ARG A 422 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" O4' A B 8 " pdb=" C1' A B 8 " pdb=" N9 A B 8 " pdb=" C4 A B 8 " ideal model delta sinusoidal sigma weight residual -106.00 -178.61 72.61 1 1.70e+01 3.46e-03 2.33e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 589 0.025 - 0.050: 259 0.050 - 0.075: 69 0.075 - 0.100: 32 0.100 - 0.124: 31 Chirality restraints: 980 Sorted by residual: chirality pdb=" CA ILE A 351 " pdb=" N ILE A 351 " pdb=" C ILE A 351 " pdb=" CB ILE A 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 977 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 455 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO A 456 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 276 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 277 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 667 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 668 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 668 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 668 " 0.022 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 492 2.16 - 2.77: 21747 2.77 - 3.38: 31525 3.38 - 3.99: 38662 3.99 - 4.60: 58960 Nonbonded interactions: 151386 Sorted by model distance: nonbonded pdb=" O SER A 105 " pdb=" HD1 HIS A 109 " model vdw 1.545 2.450 nonbonded pdb="HH21 ARG A 212 " pdb=" OE2 GLU A 214 " model vdw 1.593 2.450 nonbonded pdb=" HE ARG A 226 " pdb=" O ALA A 297 " model vdw 1.598 2.450 nonbonded pdb=" OD1 ASN A 497 " pdb=" HZ1 LYS A 536 " model vdw 1.605 2.450 nonbonded pdb="HD21 ASN A 586 " pdb=" OP1 A B -1 " model vdw 1.612 2.450 ... (remaining 151381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 6224 Z= 0.169 Angle : 0.619 19.241 8617 Z= 0.314 Chirality : 0.036 0.124 980 Planarity : 0.004 0.059 978 Dihedral : 15.947 130.863 2467 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 1.25 % Allowed : 7.65 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.31), residues: 651 helix: -0.30 (0.32), residues: 257 sheet: -1.90 (0.53), residues: 87 loop : -2.07 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 139 TYR 0.005 0.001 TYR A 88 PHE 0.007 0.001 PHE A 626 TRP 0.008 0.001 TRP A 76 HIS 0.005 0.001 HIS A 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 6220) covalent geometry : angle 0.54475 / 0.31 ( 8611) hydrogen bonds : bond 0.19162 / 12.03 ( 236) hydrogen bonds : angle 7.55376 / 5.51 ( 664) metal coordination : bond 0.10737 / 5.44 ( 4) metal coordination : angle 11.18386 / 5.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7174 (tm130) REVERT: A 172 GLU cc_start: 0.7769 (tt0) cc_final: 0.7452 (tt0) REVERT: A 276 SER cc_start: 0.8613 (p) cc_final: 0.8203 (m) REVERT: A 578 GLU cc_start: 0.8108 (tp30) cc_final: 0.7493 (tp30) REVERT: A 582 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8222 (mtt-85) REVERT: A 590 GLU cc_start: 0.7518 (tp30) cc_final: 0.7064 (tp30) outliers start: 7 outliers final: 3 residues processed: 140 average time/residue: 0.1454 time to fit residues: 27.0910 Evaluate side-chains 115 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086356 restraints weight = 42658.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089830 restraints weight = 15638.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091830 restraints weight = 7633.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.093007 restraints weight = 4646.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093679 restraints weight = 3388.094| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6224 Z= 0.165 Angle : 0.620 10.335 8617 Z= 0.322 Chirality : 0.039 0.135 980 Planarity : 0.005 0.050 978 Dihedral : 13.785 132.336 1177 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.96 % Allowed : 14.95 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.31), residues: 651 helix: 0.55 (0.31), residues: 262 sheet: -1.25 (0.53), residues: 87 loop : -1.87 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.012 0.002 TYR A 123 PHE 0.015 0.002 PHE A 423 TRP 0.008 0.001 TRP A 322 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6220) covalent geometry : angle 0.60444 / 0.32 ( 8611) hydrogen bonds : bond 0.05254 / 3.41 ( 236) hydrogen bonds : angle 5.20604 / 3.81 ( 664) metal coordination : bond 0.00673 / 0.35 ( 4) metal coordination : angle 5.22131 / 2.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.8263 (mtp-110) REVERT: A 276 SER cc_start: 0.8618 (p) cc_final: 0.8230 (m) REVERT: A 283 MET cc_start: 0.7581 (mmp) cc_final: 0.7344 (mmm) REVERT: A 394 ASP cc_start: 0.8325 (t0) cc_final: 0.8077 (t0) REVERT: A 578 GLU cc_start: 0.8064 (tp30) cc_final: 0.7681 (tp30) REVERT: A 590 GLU cc_start: 0.7560 (tp30) cc_final: 0.7079 (tp30) outliers start: 11 outliers final: 10 residues processed: 127 average time/residue: 0.1423 time to fit residues: 23.8705 Evaluate side-chains 126 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 280 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** 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 = 0.3641 r_free = 0.3641 target = 0.103318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087106 restraints weight = 42382.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090670 restraints weight = 15464.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.092725 restraints weight = 7579.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093932 restraints weight = 4631.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094471 restraints weight = 3373.740| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6224 Z= 0.119 Angle : 0.574 11.074 8617 Z= 0.291 Chirality : 0.038 0.133 980 Planarity : 0.005 0.045 978 Dihedral : 13.603 129.037 1177 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 15.84 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.32), residues: 651 helix: 1.15 (0.32), residues: 266 sheet: -1.06 (0.56), residues: 82 loop : -1.58 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.007 0.001 TYR A 250 PHE 0.013 0.002 PHE A 423 TRP 0.007 0.001 TRP A 112 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6220) covalent geometry : angle 0.54865 / 0.29 ( 8611) hydrogen bonds : bond 0.04476 / 2.97 ( 236) hydrogen bonds : angle 4.73150 / 3.49 ( 664) metal coordination : bond 0.02365 / 1.22 ( 4) metal coordination : angle 6.41117 / 3.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 SER cc_start: 0.8653 (p) cc_final: 0.8189 (m) REVERT: A 296 ASP cc_start: 0.7745 (t0) cc_final: 0.7429 (t0) REVERT: A 536 LYS cc_start: 0.2060 (OUTLIER) cc_final: 0.1739 (mttm) REVERT: A 578 GLU cc_start: 0.8116 (tp30) cc_final: 0.7747 (tp30) outliers start: 15 outliers final: 11 residues processed: 125 average time/residue: 0.1503 time to fit residues: 24.9404 Evaluate side-chains 125 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085925 restraints weight = 42521.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089487 restraints weight = 15553.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.091514 restraints weight = 7595.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092724 restraints weight = 4638.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093230 restraints weight = 3380.781| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6224 Z= 0.142 Angle : 0.579 8.764 8617 Z= 0.294 Chirality : 0.037 0.125 980 Planarity : 0.005 0.042 978 Dihedral : 13.657 129.511 1177 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.20 % Allowed : 15.66 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.33), residues: 651 helix: 1.55 (0.32), residues: 266 sheet: -0.86 (0.64), residues: 70 loop : -1.39 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 240 TYR 0.008 0.001 TYR A 224 PHE 0.011 0.002 PHE A 423 TRP 0.007 0.001 TRP A 322 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6220) covalent geometry : angle 0.56145 / 0.29 ( 8611) hydrogen bonds : bond 0.04179 / 2.79 ( 236) hydrogen bonds : angle 4.49286 / 3.31 ( 664) metal coordination : bond 0.01355 / 0.71 ( 4) metal coordination : angle 5.38103 / 2.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 394 ASP cc_start: 0.8314 (t0) cc_final: 0.8089 (t0) REVERT: A 536 LYS cc_start: 0.2420 (OUTLIER) cc_final: 0.2149 (mttm) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.1446 time to fit residues: 24.8781 Evaluate side-chains 129 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086747 restraints weight = 42267.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090350 restraints weight = 15261.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092408 restraints weight = 7428.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093636 restraints weight = 4501.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094360 restraints weight = 3279.046| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6224 Z= 0.108 Angle : 0.546 6.489 8617 Z= 0.278 Chirality : 0.037 0.127 980 Planarity : 0.004 0.040 978 Dihedral : 13.511 128.612 1177 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.02 % Allowed : 17.62 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.34), residues: 651 helix: 1.83 (0.33), residues: 266 sheet: -0.73 (0.65), residues: 70 loop : -1.33 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 240 TYR 0.020 0.002 TYR A 224 PHE 0.008 0.001 PHE A 517 TRP 0.007 0.001 TRP A 76 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6220) covalent geometry : angle 0.53481 / 0.28 ( 8611) hydrogen bonds : bond 0.03873 / 2.62 ( 236) hydrogen bonds : angle 4.36750 / 3.24 ( 664) metal coordination : bond 0.00852 / 0.45 ( 4) metal coordination : angle 4.15148 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7840 (t0) cc_final: 0.7322 (t0) REVERT: A 394 ASP cc_start: 0.8335 (t0) cc_final: 0.8105 (t0) REVERT: A 424 THR cc_start: 0.8487 (m) cc_final: 0.8257 (p) REVERT: A 536 LYS cc_start: 0.2439 (OUTLIER) cc_final: 0.2193 (mttm) REVERT: A 578 GLU cc_start: 0.8188 (tp30) cc_final: 0.7918 (tp30) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 0.1387 time to fit residues: 23.5324 Evaluate side-chains 126 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087503 restraints weight = 42293.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091039 restraints weight = 15239.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093062 restraints weight = 7393.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094265 restraints weight = 4496.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.094796 restraints weight = 3277.979| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6224 Z= 0.104 Angle : 0.527 5.952 8617 Z= 0.269 Chirality : 0.036 0.127 980 Planarity : 0.004 0.039 978 Dihedral : 13.365 127.451 1177 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.34), residues: 651 helix: 2.04 (0.33), residues: 266 sheet: -0.75 (0.63), residues: 70 loop : -1.30 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 240 TYR 0.015 0.001 TYR A 224 PHE 0.017 0.001 PHE A 423 TRP 0.008 0.001 TRP A 76 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 6220) covalent geometry : angle 0.51729 / 0.27 ( 8611) hydrogen bonds : bond 0.03613 / 2.46 ( 236) hydrogen bonds : angle 4.14023 / 3.07 ( 664) metal coordination : bond 0.00729 / 0.38 ( 4) metal coordination : angle 3.87374 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7803 (t0) cc_final: 0.7297 (t0) REVERT: A 394 ASP cc_start: 0.8374 (t0) cc_final: 0.8167 (t0) REVERT: A 516 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6840 (t80) REVERT: A 578 GLU cc_start: 0.8198 (tp30) cc_final: 0.7913 (tp30) outliers start: 17 outliers final: 15 residues processed: 127 average time/residue: 0.1354 time to fit residues: 23.0977 Evaluate side-chains 130 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 46 optimal weight: 0.0010 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087379 restraints weight = 42444.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.090905 restraints weight = 15296.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092909 restraints weight = 7411.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094100 restraints weight = 4502.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.094772 restraints weight = 3289.256| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6224 Z= 0.108 Angle : 0.535 10.081 8617 Z= 0.272 Chirality : 0.036 0.126 980 Planarity : 0.004 0.040 978 Dihedral : 13.316 127.259 1177 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.38 % Allowed : 17.62 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.34), residues: 651 helix: 2.24 (0.33), residues: 265 sheet: -0.98 (0.59), residues: 80 loop : -1.12 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.013 0.001 TYR A 364 PHE 0.016 0.001 PHE A 423 TRP 0.007 0.001 TRP A 322 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6220) covalent geometry : angle 0.52632 / 0.27 ( 8611) hydrogen bonds : bond 0.03578 / 2.41 ( 236) hydrogen bonds : angle 4.04765 / 2.99 ( 664) metal coordination : bond 0.00719 / 0.38 ( 4) metal coordination : angle 3.75153 / 1.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7832 (t0) cc_final: 0.7324 (t0) REVERT: A 394 ASP cc_start: 0.8359 (t0) cc_final: 0.8157 (t0) REVERT: A 578 GLU cc_start: 0.8195 (tp30) cc_final: 0.7910 (tp30) outliers start: 19 outliers final: 17 residues processed: 125 average time/residue: 0.1343 time to fit residues: 22.5952 Evaluate side-chains 131 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085267 restraints weight = 43080.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088697 restraints weight = 15463.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090667 restraints weight = 7518.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.091767 restraints weight = 4574.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092495 restraints weight = 3382.896| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6224 Z= 0.152 Angle : 0.554 8.618 8617 Z= 0.283 Chirality : 0.037 0.124 980 Planarity : 0.005 0.044 978 Dihedral : 13.396 128.986 1177 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.38 % Allowed : 18.15 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.34), residues: 651 helix: 2.20 (0.33), residues: 265 sheet: -1.46 (0.52), residues: 94 loop : -1.28 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.023 0.002 TYR A 90 PHE 0.017 0.002 PHE A 423 TRP 0.010 0.001 TRP A 322 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6220) covalent geometry : angle 0.54150 / 0.28 ( 8611) hydrogen bonds : bond 0.03745 / 2.50 ( 236) hydrogen bonds : angle 4.09952 / 3.02 ( 664) metal coordination : bond 0.00926 / 0.48 ( 4) metal coordination : angle 4.53917 / 2.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7976 (t0) cc_final: 0.7456 (t0) REVERT: A 482 PHE cc_start: 0.8584 (m-80) cc_final: 0.8358 (m-80) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.1361 time to fit residues: 23.4565 Evaluate side-chains 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086132 restraints weight = 42619.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089555 restraints weight = 15300.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091523 restraints weight = 7459.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092701 restraints weight = 4553.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093330 restraints weight = 3323.621| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6224 Z= 0.114 Angle : 0.540 8.338 8617 Z= 0.274 Chirality : 0.036 0.128 980 Planarity : 0.004 0.046 978 Dihedral : 13.321 127.905 1177 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.67 % Allowed : 19.04 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.34), residues: 651 helix: 2.35 (0.33), residues: 265 sheet: -1.37 (0.53), residues: 94 loop : -1.18 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.021 0.002 TYR A 123 PHE 0.018 0.001 PHE A 423 TRP 0.010 0.001 TRP A 322 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 6220) covalent geometry : angle 0.53015 / 0.27 ( 8611) hydrogen bonds : bond 0.03580 / 2.43 ( 236) hydrogen bonds : angle 3.98979 / 2.95 ( 664) metal coordination : bond 0.00703 / 0.37 ( 4) metal coordination : angle 3.92567 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.8095 (tp40) cc_final: 0.7868 (tp-100) REVERT: A 482 PHE cc_start: 0.8581 (m-80) cc_final: 0.8339 (m-80) REVERT: A 578 GLU cc_start: 0.8180 (tp30) cc_final: 0.7913 (tp30) outliers start: 15 outliers final: 15 residues processed: 132 average time/residue: 0.1305 time to fit residues: 22.9998 Evaluate side-chains 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083341 restraints weight = 43191.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086717 restraints weight = 15686.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088658 restraints weight = 7693.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.089806 restraints weight = 4698.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090457 restraints weight = 3449.909| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6224 Z= 0.181 Angle : 0.584 8.052 8617 Z= 0.299 Chirality : 0.039 0.199 980 Planarity : 0.005 0.053 978 Dihedral : 13.483 129.891 1177 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.85 % Allowed : 19.93 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.33), residues: 651 helix: 2.18 (0.33), residues: 265 sheet: -1.59 (0.49), residues: 94 loop : -1.34 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 366 TYR 0.016 0.002 TYR A 224 PHE 0.018 0.002 PHE A 423 TRP 0.015 0.001 TRP A 322 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6220) covalent geometry : angle 0.56966 / 0.30 ( 8611) hydrogen bonds : bond 0.03850 / 2.57 ( 236) hydrogen bonds : angle 4.16520 / 3.07 ( 664) metal coordination : bond 0.01027 / 0.54 ( 4) metal coordination : angle 4.91063 / 2.61 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7799 (t0) cc_final: 0.7010 (t0) REVERT: A 578 GLU cc_start: 0.8185 (tp30) cc_final: 0.7920 (tp30) outliers start: 16 outliers final: 15 residues processed: 124 average time/residue: 0.1383 time to fit residues: 23.0708 Evaluate side-chains 131 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 679 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082248 restraints weight = 43188.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085635 restraints weight = 15606.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087571 restraints weight = 7631.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088715 restraints weight = 4675.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089370 restraints weight = 3436.935| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6224 Z= 0.188 Angle : 0.592 8.220 8617 Z= 0.303 Chirality : 0.038 0.138 980 Planarity : 0.005 0.054 978 Dihedral : 13.606 131.022 1177 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.85 % Allowed : 20.64 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.33), residues: 651 helix: 2.04 (0.33), residues: 265 sheet: -1.64 (0.48), residues: 94 loop : -1.44 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 314 TYR 0.016 0.002 TYR A 224 PHE 0.016 0.002 PHE A 423 TRP 0.023 0.002 TRP A 308 HIS 0.005 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 6220) covalent geometry : angle 0.57741 / 0.30 ( 8611) hydrogen bonds : bond 0.03946 / 2.60 ( 236) hydrogen bonds : angle 4.16897 / 3.08 ( 664) metal coordination : bond 0.01023 / 0.53 ( 4) metal coordination : angle 4.99407 / 2.65 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.64 seconds wall clock time: 34 minutes 36.41 seconds (2076.41 seconds total)