Starting phenix.real_space_refine on Thu Jul 2 22:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zoy_60322/07_2026/8zoy_60322_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zoy_60322/07_2026/8zoy_60322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2026/8zoy_60322_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2026/8zoy_60322_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2026/8zoy_60322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zoy_60322/07_2026/8zoy_60322.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 Cl 1 4.86 5 C 3568 2.51 5 N 843 2.21 5 O 1004 1.98 5 H 5260 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 10701 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8768 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 547, 8749 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 547, 8749 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 2 bond proxies already assigned to first conformer: 8870 Chain: "B" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1822 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 102 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'LNR': 1, 'PTY': 1} Classifications: {'undetermined': 2, 'water': 62} Link IDs: {None: 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 101 " occ=0.45 ... (36 atoms not shown) pdb=" HZ BPHE A 101 " occ=0.55 Time building chain proxies: 2.82, per 1000 atoms: 0.26 Number of scatterers: 10701 At special positions: 0 Unit cell: (96.6, 70.84, 97.52, 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) Cl 1 17.00 S 24 16.00 P 1 15.00 O 1004 8.00 N 843 7.00 C 3568 6.00 H 5260 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 449.2 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 4 sheets defined 68.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.577A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 121 Proline residue: A 97 - end of helix removed outlier: 4.917A pdb=" N MET A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.605A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.756A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.449A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 380 removed outlier: 4.588A pdb=" N ALA A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 398 Proline residue: A 392 - end of helix removed outlier: 3.634A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.536A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.623A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.508A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.874A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.091A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.013A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 5.912A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER B 119 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 12 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 removed outlier: 5.912A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER B 119 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 12 " --> pdb=" O SER B 119 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5253 1.03 - 1.23: 36 1.23 - 1.42: 2436 1.42 - 1.62: 3031 1.62 - 1.81: 39 Bond restraints: 10795 Sorted by residual: bond pdb=" CAG LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.384 1.525 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" CAF LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" CAE LNR A 701 " pdb=" CAI LNR A 701 " ideal model delta sigma weight residual 1.384 1.519 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" CAI LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.402 1.315 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" CAE LNR A 701 " pdb=" CAF LNR A 701 " ideal model delta sigma weight residual 1.392 1.308 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 10790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 18151 1.19 - 2.39: 1163 2.39 - 3.58: 59 3.58 - 4.77: 28 4.77 - 5.96: 5 Bond angle restraints: 19406 Sorted by residual: angle pdb=" N ILE A 265 " pdb=" CA ILE A 265 " pdb=" C ILE A 265 " ideal model delta sigma weight residual 111.62 108.26 3.36 7.90e-01 1.60e+00 1.81e+01 angle pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 112.00 107.29 4.71 1.40e+00 5.10e-01 1.13e+01 angle pdb=" N PRO B 87 " pdb=" CD PRO B 87 " pdb=" CG PRO B 87 " ideal model delta sigma weight residual 103.20 98.68 4.52 1.50e+00 4.44e-01 9.09e+00 angle pdb=" C PRO A 83 " pdb=" N TYR A 84 " pdb=" CA TYR A 84 " ideal model delta sigma weight residual 121.66 117.75 3.91 1.76e+00 3.23e-01 4.93e+00 angle pdb=" CA TYR A 84 " pdb=" CB TYR A 84 " pdb=" CG TYR A 84 " ideal model delta sigma weight residual 113.90 117.82 -3.92 1.80e+00 3.09e-01 4.74e+00 ... (remaining 19401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4572 16.02 - 32.04: 358 32.04 - 48.06: 122 48.06 - 64.08: 70 64.08 - 80.09: 6 Dihedral angle restraints: 5128 sinusoidal: 2619 harmonic: 2509 Sorted by residual: dihedral pdb=" CA TRP A 128 " pdb=" C TRP A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP B 61 " pdb=" CB ASP B 61 " pdb=" CG ASP B 61 " pdb=" OD1 ASP B 61 " ideal model delta sinusoidal sigma weight residual -30.00 -86.96 56.96 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA PHE A 409 " pdb=" C PHE A 409 " pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta harmonic sigma weight residual 180.00 164.51 15.49 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 5125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 612 0.043 - 0.086: 170 0.086 - 0.129: 42 0.129 - 0.172: 3 0.172 - 0.214: 1 Chirality restraints: 828 Sorted by residual: chirality pdb=" CAL LNR A 701 " pdb=" CAH LNR A 701 " pdb=" CAK LNR A 701 " pdb=" OAD LNR A 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.50 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PRO A 83 " pdb=" N PRO A 83 " pdb=" C PRO A 83 " pdb=" CB PRO A 83 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 825 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU A 102 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " -0.052 5.00e-02 4.00e+02 7.60e-02 9.23e+00 pdb=" N PRO B 87 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 214 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C TYR A 214 " -0.033 2.00e-02 2.50e+03 pdb=" O TYR A 214 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 215 " 0.011 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 700 2.20 - 2.80: 22286 2.80 - 3.40: 32321 3.40 - 4.00: 44441 4.00 - 4.60: 67646 Nonbonded interactions: 167394 Sorted by model distance: nonbonded pdb=" OD1 ASP A 298 " pdb=" H ASP A 298 " model vdw 1.594 2.450 nonbonded pdb=" HZ2 LYS A 522 " pdb=" O ALA A 616 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU B 6 " pdb=" H CYS B 95 " model vdw 1.630 2.450 nonbonded pdb="HE21 GLN A 234 " pdb=" OE1 GLN A 236 " model vdw 1.633 2.450 nonbonded pdb=" H PHE A 335 " pdb=" OH TYR B 107 " model vdw 1.635 2.450 ... (remaining 167389 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.007 0.141 5537 Z= 0.306 Angle : 0.647 5.963 7544 Z= 0.372 Chirality : 0.042 0.214 828 Planarity : 0.006 0.076 924 Dihedral : 15.324 80.094 1886 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.07 % Allowed : 13.37 % Favored : 85.56 % 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: 0.87 (0.33), residues: 661 helix: 0.80 (0.27), residues: 375 sheet: -0.60 (0.78), residues: 33 loop : 0.67 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 216 TYR 0.021 0.002 TYR A 572 PHE 0.024 0.002 PHE A 316 TRP 0.013 0.002 TRP A 80 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.31 ( 5535) covalent geometry : angle 0.64611 / 0.37 ( 7540) SS BOND : bond 0.00432 / 0.27 ( 2) SS BOND : angle 1.49952 / 0.69 ( 4) hydrogen bonds : bond 0.14191 / 9.08 ( 335) hydrogen bonds : angle 6.88580 / 4.90 ( 958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7561 (mp0) REVERT: A 607 ARG cc_start: 0.8065 (ptp-170) cc_final: 0.7803 (ptm160) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 1.0432 time to fit residues: 96.4263 Evaluate side-chains 86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 436 GLN A 581 GLN A 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117592 restraints weight = 18153.665| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.38 r_work: 0.3274 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5537 Z= 0.209 Angle : 0.576 5.245 7544 Z= 0.313 Chirality : 0.040 0.138 828 Planarity : 0.006 0.058 924 Dihedral : 8.559 79.879 759 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.78 % Allowed : 13.55 % Favored : 84.67 % 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: 1.10 (0.34), residues: 661 helix: 0.98 (0.26), residues: 380 sheet: -0.53 (0.87), residues: 33 loop : 0.79 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 518 TYR 0.018 0.002 TYR A 572 PHE 0.021 0.002 PHE A 316 TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 5535) covalent geometry : angle 0.57547 / 0.31 ( 7540) SS BOND : bond 0.00403 / 0.25 ( 2) SS BOND : angle 1.32222 / 0.59 ( 4) hydrogen bonds : bond 0.05054 / 3.28 ( 335) hydrogen bonds : angle 5.71537 / 4.17 ( 958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7835 (mp0) REVERT: A 377 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: A 607 ARG cc_start: 0.8187 (ptp-170) cc_final: 0.7951 (ptm160) REVERT: B 39 GLN cc_start: 0.8570 (tp40) cc_final: 0.8358 (tp40) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 1.0327 time to fit residues: 98.7277 Evaluate side-chains 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106374 restraints weight = 17968.007| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.46 r_work: 0.3048 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5537 Z= 0.139 Angle : 0.512 5.062 7544 Z= 0.275 Chirality : 0.037 0.132 828 Planarity : 0.005 0.043 924 Dihedral : 7.229 78.113 755 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.89 % Allowed : 13.90 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.34), residues: 661 helix: 1.24 (0.27), residues: 381 sheet: -0.64 (0.77), residues: 40 loop : 0.84 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.015 0.001 TYR A 84 PHE 0.015 0.002 PHE A 316 TRP 0.009 0.001 TRP A 128 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 5535) covalent geometry : angle 0.51157 / 0.28 ( 7540) SS BOND : bond 0.00272 / 0.17 ( 2) SS BOND : angle 1.06021 / 0.49 ( 4) hydrogen bonds : bond 0.04287 / 2.77 ( 335) hydrogen bonds : angle 5.30308 / 3.89 ( 958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7804 (mp0) REVERT: A 377 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: A 607 ARG cc_start: 0.8085 (ptp-170) cc_final: 0.7859 (ptm160) REVERT: B 83 ASN cc_start: 0.8534 (m-40) cc_final: 0.8225 (m-40) outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 1.0100 time to fit residues: 100.9069 Evaluate side-chains 89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 19 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103587 restraints weight = 19329.925| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.54 r_work: 0.3013 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5537 Z= 0.174 Angle : 0.530 5.090 7544 Z= 0.288 Chirality : 0.039 0.135 828 Planarity : 0.005 0.045 924 Dihedral : 7.171 75.781 753 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.25 % Allowed : 14.26 % Favored : 84.49 % 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: 1.32 (0.34), residues: 661 helix: 1.23 (0.27), residues: 382 sheet: -0.63 (0.76), residues: 40 loop : 0.83 (0.45), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 216 TYR 0.014 0.002 TYR A 84 PHE 0.019 0.002 PHE A 316 TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 5535) covalent geometry : angle 0.52964 / 0.29 ( 7540) SS BOND : bond 0.00340 / 0.21 ( 2) SS BOND : angle 1.25169 / 0.59 ( 4) hydrogen bonds : bond 0.04532 / 2.93 ( 335) hydrogen bonds : angle 5.36150 / 3.92 ( 958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7814 (mp0) REVERT: A 377 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: A 607 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7805 (ptm160) REVERT: B 83 ASN cc_start: 0.8567 (m-40) cc_final: 0.8294 (m-40) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.9650 time to fit residues: 90.6737 Evaluate side-chains 90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106354 restraints weight = 17234.017| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.42 r_work: 0.3047 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5537 Z= 0.141 Angle : 0.503 5.303 7544 Z= 0.271 Chirality : 0.037 0.134 828 Planarity : 0.005 0.044 924 Dihedral : 6.779 74.657 751 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.25 % Allowed : 14.26 % Favored : 84.49 % 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: 1.45 (0.34), residues: 661 helix: 1.32 (0.27), residues: 382 sheet: -0.54 (0.74), residues: 40 loop : 0.88 (0.45), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.014 0.001 TYR A 84 PHE 0.015 0.001 PHE A 316 TRP 0.009 0.001 TRP A 128 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 5535) covalent geometry : angle 0.50218 / 0.27 ( 7540) SS BOND : bond 0.00307 / 0.19 ( 2) SS BOND : angle 1.02048 / 0.47 ( 4) hydrogen bonds : bond 0.04180 / 2.70 ( 335) hydrogen bonds : angle 5.18850 / 3.81 ( 958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7840 (mp0) REVERT: A 377 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: A 421 MET cc_start: 0.8439 (mtm) cc_final: 0.8204 (mtm) REVERT: B 83 ASN cc_start: 0.8578 (m-40) cc_final: 0.8325 (m-40) outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.9338 time to fit residues: 86.8579 Evaluate side-chains 87 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104907 restraints weight = 21811.359| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.64 r_work: 0.3031 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5537 Z= 0.139 Angle : 0.498 5.162 7544 Z= 0.268 Chirality : 0.037 0.133 828 Planarity : 0.005 0.045 924 Dihedral : 6.552 73.384 751 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.07 % Allowed : 14.26 % Favored : 84.67 % 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: 1.55 (0.34), residues: 661 helix: 1.41 (0.27), residues: 382 sheet: -0.52 (0.72), residues: 40 loop : 0.93 (0.45), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 607 TYR 0.014 0.001 TYR A 391 PHE 0.015 0.001 PHE A 316 TRP 0.010 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5535) covalent geometry : angle 0.49744 / 0.27 ( 7540) SS BOND : bond 0.00305 / 0.18 ( 2) SS BOND : angle 1.03207 / 0.48 ( 4) hydrogen bonds : bond 0.04115 / 2.66 ( 335) hydrogen bonds : angle 5.12085 / 3.77 ( 958) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.297 Fit side-chains REVERT: A 168 THR cc_start: 0.8423 (p) cc_final: 0.8189 (t) REVERT: A 304 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7810 (mp0) REVERT: A 377 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: B 83 ASN cc_start: 0.8559 (m-40) cc_final: 0.8306 (m-40) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.9122 time to fit residues: 84.0091 Evaluate side-chains 86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105710 restraints weight = 18889.085| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.53 r_work: 0.3033 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5537 Z= 0.141 Angle : 0.501 5.216 7544 Z= 0.269 Chirality : 0.037 0.133 828 Planarity : 0.005 0.044 924 Dihedral : 6.461 72.982 751 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.25 % Allowed : 14.44 % Favored : 84.31 % 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: 1.61 (0.34), residues: 661 helix: 1.51 (0.27), residues: 378 sheet: -0.45 (0.71), residues: 40 loop : 0.86 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.015 0.001 TYR A 391 PHE 0.015 0.001 PHE A 316 TRP 0.009 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 5535) covalent geometry : angle 0.50072 / 0.27 ( 7540) SS BOND : bond 0.00317 / 0.19 ( 2) SS BOND : angle 0.98829 / 0.46 ( 4) hydrogen bonds : bond 0.04126 / 2.66 ( 335) hydrogen bonds : angle 5.09881 / 3.76 ( 958) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8432 (p) cc_final: 0.8202 (t) REVERT: A 304 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7820 (mp0) REVERT: A 377 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: B 83 ASN cc_start: 0.8550 (m-40) cc_final: 0.8309 (m-40) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 1.0287 time to fit residues: 90.9674 Evaluate side-chains 86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN B 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105370 restraints weight = 17895.105| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.49 r_work: 0.3006 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5537 Z= 0.154 Angle : 0.506 5.206 7544 Z= 0.273 Chirality : 0.038 0.132 828 Planarity : 0.005 0.045 924 Dihedral : 6.491 72.423 751 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.71 % Allowed : 14.80 % Favored : 84.49 % 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: 1.55 (0.34), residues: 661 helix: 1.46 (0.27), residues: 378 sheet: -0.41 (0.70), residues: 40 loop : 0.82 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.015 0.001 TYR A 391 PHE 0.017 0.002 PHE A 316 TRP 0.012 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5535) covalent geometry : angle 0.50583 / 0.27 ( 7540) SS BOND : bond 0.00323 / 0.20 ( 2) SS BOND : angle 1.09563 / 0.51 ( 4) hydrogen bonds : bond 0.04230 / 2.73 ( 335) hydrogen bonds : angle 5.14512 / 3.79 ( 958) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.319 Fit side-chains REVERT: A 304 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7805 (mp0) REVERT: A 377 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: B 83 ASN cc_start: 0.8512 (m-40) cc_final: 0.8277 (m-40) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 1.0160 time to fit residues: 88.7682 Evaluate side-chains 84 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104173 restraints weight = 19995.310| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.57 r_work: 0.2988 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5537 Z= 0.162 Angle : 0.512 5.225 7544 Z= 0.277 Chirality : 0.038 0.132 828 Planarity : 0.005 0.045 924 Dihedral : 6.533 71.704 751 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.89 % Allowed : 14.80 % Favored : 84.31 % 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: 1.54 (0.34), residues: 661 helix: 1.45 (0.27), residues: 378 sheet: -0.36 (0.70), residues: 40 loop : 0.81 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.016 0.001 TYR A 391 PHE 0.018 0.002 PHE A 316 TRP 0.011 0.001 TRP A 556 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5535) covalent geometry : angle 0.51152 / 0.28 ( 7540) SS BOND : bond 0.00346 / 0.21 ( 2) SS BOND : angle 1.11590 / 0.52 ( 4) hydrogen bonds : bond 0.04315 / 2.79 ( 335) hydrogen bonds : angle 5.18246 / 3.82 ( 958) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.275 Fit side-chains REVERT: A 304 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7805 (mp0) REVERT: A 377 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: B 83 ASN cc_start: 0.8521 (m-40) cc_final: 0.8268 (m-40) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.9425 time to fit residues: 79.5859 Evaluate side-chains 82 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105542 restraints weight = 21171.321| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.61 r_work: 0.3008 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5537 Z= 0.133 Angle : 0.493 5.313 7544 Z= 0.266 Chirality : 0.037 0.132 828 Planarity : 0.005 0.044 924 Dihedral : 6.369 71.585 751 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.71 % Allowed : 14.80 % Favored : 84.49 % 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: 1.62 (0.34), residues: 661 helix: 1.51 (0.27), residues: 378 sheet: -0.24 (0.70), residues: 40 loop : 0.83 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.015 0.001 TYR A 84 PHE 0.014 0.001 PHE A 316 TRP 0.013 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 5535) covalent geometry : angle 0.49296 / 0.27 ( 7540) SS BOND : bond 0.00298 / 0.18 ( 2) SS BOND : angle 0.92963 / 0.43 ( 4) hydrogen bonds : bond 0.04054 / 2.61 ( 335) hydrogen bonds : angle 5.05834 / 3.74 ( 958) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7851 (mp0) REVERT: A 377 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: B 83 ASN cc_start: 0.8573 (m-40) cc_final: 0.8331 (m-40) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.8667 time to fit residues: 77.1991 Evaluate side-chains 84 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 50 optimal weight: 0.0570 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 350 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108653 restraints weight = 18101.183| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.50 r_work: 0.3062 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5537 Z= 0.110 Angle : 0.478 5.229 7544 Z= 0.256 Chirality : 0.037 0.130 828 Planarity : 0.005 0.043 924 Dihedral : 6.144 71.380 751 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.07 % Allowed : 14.62 % Favored : 84.31 % 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: 1.73 (0.34), residues: 661 helix: 1.62 (0.27), residues: 378 sheet: -0.39 (0.69), residues: 42 loop : 0.89 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 442 TYR 0.014 0.001 TYR A 84 PHE 0.012 0.001 PHE A 408 TRP 0.015 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 5535) covalent geometry : angle 0.47745 / 0.26 ( 7540) SS BOND : bond 0.00240 / 0.15 ( 2) SS BOND : angle 0.78032 / 0.37 ( 4) hydrogen bonds : bond 0.03772 / 2.42 ( 335) hydrogen bonds : angle 4.90378 / 3.63 ( 958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4390.20 seconds wall clock time: 75 minutes 7.71 seconds (4507.71 seconds total)