Starting phenix.real_space_refine on Fri Sep 11 23:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m5o_23678/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m5o_23678/09_2026/7m5o_23678.map" } 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-2.2.1-6174/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: {'RNAv2': 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: 1.88, 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: 1.22 Conformation dependent library (CDL) restraints added in 416.8 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: 2.06 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: 2.54 Time building geometry restraints manager: 1.64 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 - 1.03: 19570 1.03 - 2.07: 1515 2.07 - 3.10: 258 3.10 - 4.14: 61 4.14 - 5.17: 16 Bond angle restraints: 21420 Sorted by residual: angle pdb=" C3' A B 8 " pdb=" C2' A B 8 " pdb=" O2' A B 8 " ideal model delta sigma weight residual 109.80 114.97 -5.17 2.00e+00 2.50e-01 6.69e+00 angle pdb=" C3' A B -19 " pdb=" C2' A B -19 " pdb=" O2' A B -19 " ideal model delta sigma weight residual 109.80 114.84 -5.04 2.00e+00 2.50e-01 6.34e+00 angle pdb=" C3' A B -9 " pdb=" C2' A B -9 " pdb=" O2' A B -9 " ideal model delta sigma weight residual 109.80 114.78 -4.98 2.00e+00 2.50e-01 6.21e+00 angle pdb=" C3' A B 9 " pdb=" C2' A B 9 " pdb=" O2' A B 9 " ideal model delta sigma weight residual 109.80 114.74 -4.94 2.00e+00 2.50e-01 6.11e+00 angle pdb=" C3' G B 13 " pdb=" C2' G B 13 " pdb=" O2' G B 13 " ideal model delta sigma weight residual 109.80 114.70 -4.90 2.00e+00 2.50e-01 5.99e+00 ... (remaining 21415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4783 17.42 - 34.84: 429 34.84 - 52.26: 136 52.26 - 69.68: 87 69.68 - 87.10: 24 Dihedral angle restraints: 5459 sinusoidal: 3260 harmonic: 2199 Sorted by residual: dihedral pdb=" C4' A B -19 " pdb=" C3' A B -19 " pdb=" C2' A B -19 " pdb=" C1' A B -19 " ideal model delta sinusoidal sigma weight residual 36.34 -36.99 73.34 1 3.10e+00 1.04e-01 7.12e+02 dihedral pdb=" C4' A B 8 " pdb=" C3' A B 8 " pdb=" C2' A B 8 " pdb=" C1' A B 8 " ideal model delta sinusoidal sigma weight residual 36.34 -36.91 73.26 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' A B -9 " pdb=" C3' A B -9 " pdb=" C2' A B -9 " pdb=" C1' A B -9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.56 72.91 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 796 0.057 - 0.114: 115 0.114 - 0.171: 10 0.171 - 0.229: 26 0.229 - 0.286: 33 Chirality restraints: 980 Sorted by residual: chirality pdb=" C2' A B -9 " pdb=" C3' A B -9 " pdb=" O2' A B -9 " pdb=" C1' A B -9 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' A B 8 " pdb=" C3' A B 8 " pdb=" O2' A B 8 " pdb=" C1' A B 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' C B -21 " pdb=" C3' C B -21 " pdb=" O2' C B -21 " pdb=" C1' C B -21 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.070 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.820 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- 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= 0.177 Angle : 0.742 19.241 8617 Z= 0.353 Chirality : 0.069 0.286 980 Planarity : 0.004 0.059 978 Dihedral : 17.932 87.095 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 0.00309 / 0.15 ( 6220) covalent geometry : angle 0.68112 / 0.35 ( 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 : 0.286 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: 0.1686 time to fit residues: 31.5323 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 : 0.297 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.0570 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.102634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086969 restraints weight = 42805.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090473 restraints weight = 15692.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092487 restraints weight = 7660.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093679 restraints weight = 4644.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094419 restraints weight = 3397.405| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6224 Z= 0.209 Angle : 1.037 15.726 8617 Z= 0.459 Chirality : 0.084 0.822 980 Planarity : 0.006 0.051 978 Dihedral : 16.140 138.194 1177 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.78 % Allowed : 15.30 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.31), residues: 651 helix: 0.52 (0.31), residues: 261 sheet: -1.25 (0.53), residues: 87 loop : -1.87 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.011 0.002 TYR A 250 PHE 0.014 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 0.00442 / 0.21 ( 6220) covalent geometry : angle 1.02727 / 0.46 ( 8611) hydrogen bonds : bond 0.05402 / 3.51 ( 236) hydrogen bonds : angle 5.29591 / 3.87 ( 664) metal coordination : bond 0.00956 / 0.49 ( 4) metal coordination : angle 5.51068 / 3.10 ( 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 128 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.288 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: A 283 MET cc_start: 0.7218 (mmp) cc_final: 0.6939 (mmt) REVERT: A 578 GLU cc_start: 0.8043 (tp30) cc_final: 0.7769 (tp30) REVERT: A 582 ARG cc_start: 0.8559 (mtt-85) cc_final: 0.8357 (mtt-85) REVERT: A 590 GLU cc_start: 0.7539 (tp30) cc_final: 0.7067 (tp30) outliers start: 10 outliers final: 9 residues processed: 123 average time/residue: 0.1681 time to fit residues: 27.7314 Evaluate side-chains 119 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.103610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087687 restraints weight = 43050.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091224 restraints weight = 15755.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093255 restraints weight = 7740.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094488 restraints weight = 4733.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095037 restraints weight = 3448.871| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6224 Z= 0.152 Angle : 0.830 11.915 8617 Z= 0.371 Chirality : 0.061 0.596 980 Planarity : 0.005 0.049 978 Dihedral : 16.116 145.999 1176 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.85 % Allowed : 16.19 % Favored : 80.96 % 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: -0.62 (0.32), residues: 651 helix: 1.10 (0.31), residues: 266 sheet: -1.05 (0.56), residues: 82 loop : -1.65 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.012 0.002 TYR A 123 PHE 0.013 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 0.00326 / 0.15 ( 6220) covalent geometry : angle 0.81130 / 0.37 ( 8611) hydrogen bonds : bond 0.04733 / 3.16 ( 236) hydrogen bonds : angle 4.78770 / 3.52 ( 664) metal coordination : bond 0.02675 / 1.33 ( 4) metal coordination : angle 6.71343 / 3.35 ( 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 130 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.310 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 240 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.8043 (mtm110) REVERT: A 296 ASP cc_start: 0.7544 (t0) cc_final: 0.6916 (t0) REVERT: A 394 ASP cc_start: 0.8253 (t0) cc_final: 0.8046 (t0) REVERT: A 423 PHE cc_start: 0.8749 (p90) cc_final: 0.8333 (p90) REVERT: A 578 GLU cc_start: 0.8072 (tp30) cc_final: 0.7855 (tp30) REVERT: A 606 GLU cc_start: 0.7931 (pt0) cc_final: 0.7716 (pt0) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.1624 time to fit residues: 26.7220 Evaluate side-chains 124 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 276 SER 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 589 ILE 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: 0.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.101413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085500 restraints weight = 42993.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089034 restraints weight = 15825.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091081 restraints weight = 7783.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092284 restraints weight = 4767.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093010 restraints weight = 3489.948| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6224 Z= 0.179 Angle : 0.787 9.820 8617 Z= 0.360 Chirality : 0.055 0.405 980 Planarity : 0.005 0.059 978 Dihedral : 15.676 150.097 1174 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.91 % Allowed : 15.84 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.33), residues: 651 helix: 1.45 (0.32), residues: 266 sheet: -0.97 (0.62), residues: 70 loop : -1.52 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.014 0.002 TYR A 250 PHE 0.011 0.002 PHE A 423 TRP 0.010 0.001 TRP A 322 HIS 0.005 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 6220) covalent geometry : angle 0.77204 / 0.36 ( 8611) hydrogen bonds : bond 0.04431 / 2.95 ( 236) hydrogen bonds : angle 4.55798 / 3.35 ( 664) metal coordination : bond 0.01469 / 0.77 ( 4) metal coordination : angle 5.80689 / 2.88 ( 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 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.310 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 290 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 296 ASP cc_start: 0.7752 (t0) cc_final: 0.7147 (t0) REVERT: A 423 PHE cc_start: 0.8798 (p90) cc_final: 0.8596 (p90) REVERT: A 557 ASN cc_start: 0.8104 (m-40) cc_final: 0.7782 (t0) REVERT: A 578 GLU cc_start: 0.8128 (tp30) cc_final: 0.7777 (tp30) outliers start: 22 outliers final: 20 residues processed: 124 average time/residue: 0.1578 time to fit residues: 26.4623 Evaluate side-chains 132 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 276 SER 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 424 THR Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 589 ILE 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: 3.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 151 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 = 0.3595 r_free = 0.3595 target = 0.100413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084624 restraints weight = 43413.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088110 restraints weight = 15887.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090108 restraints weight = 7806.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091316 restraints weight = 4779.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091835 restraints weight = 3485.963| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6224 Z= 0.179 Angle : 0.754 7.996 8617 Z= 0.350 Chirality : 0.053 0.290 980 Planarity : 0.005 0.053 978 Dihedral : 15.632 150.857 1174 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.91 % Allowed : 16.90 % Favored : 79.18 % 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: -0.28 (0.33), residues: 651 helix: 1.61 (0.32), residues: 265 sheet: -1.10 (0.60), residues: 70 loop : -1.60 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.018 0.002 TYR A 224 PHE 0.009 0.002 PHE A 354 TRP 0.009 0.001 TRP A 322 HIS 0.005 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 6220) covalent geometry : angle 0.74207 / 0.35 ( 8611) hydrogen bonds : bond 0.04238 / 2.83 ( 236) hydrogen bonds : angle 4.48418 / 3.31 ( 664) metal coordination : bond 0.01135 / 0.59 ( 4) metal coordination : angle 5.02573 / 2.61 ( 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 136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.233 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 578 GLU cc_start: 0.8113 (tp30) cc_final: 0.7818 (tp30) outliers start: 22 outliers final: 17 residues processed: 129 average time/residue: 0.1544 time to fit residues: 26.9582 Evaluate side-chains 125 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 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 276 SER 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 589 ILE 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: 0.5980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.102422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086555 restraints weight = 42853.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090104 restraints weight = 15600.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092148 restraints weight = 7650.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093364 restraints weight = 4681.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094022 restraints weight = 3418.447| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3101 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= 0.122 Angle : 0.706 7.746 8617 Z= 0.328 Chirality : 0.050 0.240 980 Planarity : 0.005 0.053 978 Dihedral : 15.582 150.303 1174 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.56 % Allowed : 18.86 % 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: 0.05 (0.34), residues: 651 helix: 1.83 (0.33), residues: 266 sheet: -1.20 (0.61), residues: 78 loop : -1.28 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.019 0.002 TYR A 90 PHE 0.010 0.001 PHE A 636 TRP 0.009 0.001 TRP A 322 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6220) covalent geometry : angle 0.69786 / 0.33 ( 8611) hydrogen bonds : bond 0.03915 / 2.66 ( 236) hydrogen bonds : angle 4.32890 / 3.21 ( 664) metal coordination : bond 0.00779 / 0.41 ( 4) metal coordination : angle 4.08470 / 2.08 ( 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 137 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.299 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: 0.7673 (t0) cc_final: 0.7138 (t0) REVERT: A 578 GLU cc_start: 0.8070 (tp30) cc_final: 0.7765 (tp30) outliers start: 20 outliers final: 18 residues processed: 126 average time/residue: 0.1607 time to fit residues: 27.4244 Evaluate side-chains 130 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 276 SER 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 589 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.100477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084623 restraints weight = 42948.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088118 restraints weight = 15749.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090149 restraints weight = 7750.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091327 restraints weight = 4748.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092069 restraints weight = 3495.210| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3326 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= 0.161 Angle : 0.716 7.245 8617 Z= 0.332 Chirality : 0.050 0.226 980 Planarity : 0.005 0.056 978 Dihedral : 15.618 151.829 1174 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.56 % Allowed : 19.57 % Favored : 76.87 % 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: -0.10 (0.33), residues: 651 helix: 1.93 (0.32), residues: 266 sheet: -1.51 (0.51), residues: 94 loop : -1.51 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 240 TYR 0.017 0.002 TYR A 364 PHE 0.018 0.002 PHE A 423 TRP 0.011 0.001 TRP A 322 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 6220) covalent geometry : angle 0.70516 / 0.33 ( 8611) hydrogen bonds : bond 0.03971 / 2.67 ( 236) hydrogen bonds : angle 4.27922 / 3.17 ( 664) metal coordination : bond 0.00953 / 0.50 ( 4) metal coordination : angle 4.65498 / 2.45 ( 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 132 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.306 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 125 HIS cc_start: 0.7248 (t-90) cc_final: 0.7016 (t70) REVERT: A 296 ASP cc_start: 0.7712 (t0) cc_final: 0.7201 (t0) REVERT: A 410 GLN cc_start: 0.8161 (tp40) cc_final: 0.7956 (tp40) REVERT: A 578 GLU cc_start: 0.8107 (tp30) cc_final: 0.7806 (tp30) outliers start: 20 outliers final: 19 residues processed: 124 average time/residue: 0.1557 time to fit residues: 26.0072 Evaluate side-chains 130 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 GLN 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 276 SER 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 536 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.099140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083578 restraints weight = 43829.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087040 restraints weight = 16007.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089029 restraints weight = 7838.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090215 restraints weight = 4783.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.090855 restraints weight = 3485.432| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3508 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= 0.184 Angle : 0.725 8.054 8617 Z= 0.338 Chirality : 0.050 0.226 980 Planarity : 0.005 0.059 978 Dihedral : 15.649 152.207 1174 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.56 % Allowed : 20.28 % Favored : 76.16 % 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 (0.33), residues: 651 helix: 1.84 (0.32), residues: 266 sheet: -1.65 (0.50), residues: 94 loop : -1.63 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.016 0.002 TYR A 224 PHE 0.016 0.002 PHE A 423 TRP 0.014 0.001 TRP A 322 HIS 0.004 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 6220) covalent geometry : angle 0.71309 / 0.34 ( 8611) hydrogen bonds : bond 0.04058 / 2.73 ( 236) hydrogen bonds : angle 4.31989 / 3.20 ( 664) metal coordination : bond 0.01007 / 0.53 ( 4) metal coordination : angle 4.98780 / 2.65 ( 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 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.298 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: A 564 LYS cc_start: 0.6991 (pttt) cc_final: 0.6675 (pttp) outliers start: 20 outliers final: 18 residues processed: 125 average time/residue: 0.1612 time to fit residues: 27.1290 Evaluate side-chains 128 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 GLN 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 276 SER 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 536 LYS Chi-restraints excluded: chain A residue 658 VAL 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: 0.9990 chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.100704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084971 restraints weight = 42618.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088501 restraints weight = 15611.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090519 restraints weight = 7678.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091751 restraints weight = 4709.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092470 restraints weight = 3405.053| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6224 Z= 0.131 Angle : 0.687 7.643 8617 Z= 0.321 Chirality : 0.049 0.226 980 Planarity : 0.005 0.053 978 Dihedral : 15.581 150.887 1174 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.02 % Allowed : 21.35 % Favored : 75.62 % 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: 266 sheet: -1.46 (0.51), residues: 94 loop : -1.53 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.015 0.002 TYR A 224 PHE 0.016 0.002 PHE A 423 TRP 0.026 0.002 TRP A 308 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6220) covalent geometry : angle 0.67933 / 0.32 ( 8611) hydrogen bonds : bond 0.03792 / 2.56 ( 236) hydrogen bonds : angle 4.18377 / 3.11 ( 664) metal coordination : bond 0.00640 / 0.33 ( 4) metal coordination : angle 3.89876 / 2.01 ( 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 131 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 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: A 125 HIS cc_start: 0.7329 (t-90) cc_final: 0.7050 (t70) REVERT: A 296 ASP cc_start: 0.7568 (t0) cc_final: 0.6658 (t0) REVERT: A 410 GLN cc_start: 0.8109 (tp40) cc_final: 0.7881 (tp40) REVERT: A 536 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2954 (mttm) REVERT: A 578 GLU cc_start: 0.8110 (tp30) cc_final: 0.7799 (tp30) REVERT: A 711 LYS cc_start: 0.8912 (mttt) cc_final: 0.8242 (pptt) outliers start: 17 outliers final: 16 residues processed: 124 average time/residue: 0.1573 time to fit residues: 26.1242 Evaluate side-chains 128 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 276 SER 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 536 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** A 386 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 = 0.3591 r_free = 0.3591 target = 0.099713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084095 restraints weight = 43047.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087566 restraints weight = 15746.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089570 restraints weight = 7712.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090771 restraints weight = 4711.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091387 restraints weight = 3417.947| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6224 Z= 0.159 Angle : 0.706 8.250 8617 Z= 0.330 Chirality : 0.049 0.221 980 Planarity : 0.005 0.051 978 Dihedral : 15.620 151.275 1174 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.20 % Allowed : 21.53 % Favored : 75.27 % 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: -0.09 (0.33), residues: 651 helix: 1.96 (0.32), residues: 266 sheet: -1.50 (0.50), residues: 94 loop : -1.52 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.015 0.002 TYR A 224 PHE 0.016 0.002 PHE A 423 TRP 0.016 0.001 TRP A 322 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 6220) covalent geometry : angle 0.69613 / 0.33 ( 8611) hydrogen bonds : bond 0.03856 / 2.60 ( 236) hydrogen bonds : angle 4.17736 / 3.10 ( 664) metal coordination : bond 0.00863 / 0.45 ( 4) metal coordination : angle 4.47645 / 2.34 ( 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: 18 poor density : 115 time to evaluate : 0.295 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 296 ASP cc_start: 0.7630 (t0) cc_final: 0.6742 (t0) REVERT: A 536 LYS cc_start: 0.3402 (OUTLIER) cc_final: 0.3163 (mttm) REVERT: A 578 GLU cc_start: 0.8101 (tp30) cc_final: 0.7820 (tp30) REVERT: A 590 GLU cc_start: 0.7676 (tp30) cc_final: 0.7000 (tp30) REVERT: A 711 LYS cc_start: 0.8937 (mttt) cc_final: 0.8253 (pptt) outliers start: 18 outliers final: 16 residues processed: 126 average time/residue: 0.1555 time to fit residues: 26.4474 Evaluate side-chains 130 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS 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 276 SER 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 536 LYS Chi-restraints excluded: chain A residue 658 VAL 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: 0.7980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.098816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083172 restraints weight = 43005.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086666 restraints weight = 15715.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.088692 restraints weight = 7682.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.089739 restraints weight = 4656.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090430 restraints weight = 3492.197| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6224 Z= 0.179 Angle : 0.714 8.327 8617 Z= 0.334 Chirality : 0.049 0.215 980 Planarity : 0.005 0.053 978 Dihedral : 15.651 151.485 1174 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.38 % Allowed : 21.89 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.33), residues: 651 helix: 1.84 (0.32), residues: 267 sheet: -1.66 (0.49), residues: 94 loop : -1.51 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.016 0.002 TYR A 224 PHE 0.015 0.002 PHE A 423 TRP 0.017 0.002 TRP A 322 HIS 0.003 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 6220) covalent geometry : angle 0.70383 / 0.33 ( 8611) hydrogen bonds : bond 0.03936 / 2.64 ( 236) hydrogen bonds : angle 4.20860 / 3.11 ( 664) metal coordination : bond 0.00864 / 0.45 ( 4) metal coordination : angle 4.61900 / 2.44 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.07 seconds wall clock time: 39 minutes 6.10 seconds (2346.10 seconds total)