Starting phenix.real_space_refine on Sat Nov 16 09:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zoy_60322/11_2024/8zoy_60322_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zoy_60322/11_2024/8zoy_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zoy_60322/11_2024/8zoy_60322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zoy_60322/11_2024/8zoy_60322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zoy_60322/11_2024/8zoy_60322_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zoy_60322/11_2024/8zoy_60322_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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, 103 Unusual residues: {' CL': 1, 'LNR': 1, 'PTY': 1} Classifications: {'undetermined': 3, 'water': 62} Link IDs: {None: 64} 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: 9.51, per 1000 atoms: 0.89 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: 3.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.04 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: 4.23 Time building geometry restraints manager: 3.89 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: 1.090 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: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.080 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 5535 Z= 0.404 Angle : 0.646 5.963 7540 Z= 0.371 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.013 0.002 TRP A 80 HIS 0.005 0.001 HIS A 370 PHE 0.024 0.002 PHE A 316 TYR 0.021 0.002 TYR A 572 ARG 0.005 0.001 ARG A 216 *********************** 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 : 0.863 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7857 (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: 6 residues processed: 88 average time/residue: 2.4227 time to fit residues: 224.1432 Evaluate side-chains 87 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 350 ASN 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 54 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 436 GLN A 581 GLN A 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5535 Z= 0.226 Angle : 0.546 5.166 7540 Z= 0.294 Chirality : 0.038 0.132 828 Planarity : 0.005 0.053 924 Dihedral : 8.238 79.700 761 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.60 % Allowed : 13.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.34), residues: 661 helix: 1.09 (0.26), residues: 381 sheet: -0.45 (0.88), residues: 33 loop : 0.82 (0.45), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS A 370 PHE 0.017 0.002 PHE A 316 TYR 0.017 0.002 TYR A 84 ARG 0.005 0.001 ARG A 518 *********************** 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 98 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7211 (p0) REVERT: A 304 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7625 (mp0) REVERT: A 377 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: A 607 ARG cc_start: 0.8056 (ptp-170) cc_final: 0.7833 (ptm160) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 2.3679 time to fit residues: 231.2920 Evaluate side-chains 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5535 Z= 0.195 Angle : 0.511 4.810 7540 Z= 0.275 Chirality : 0.038 0.133 828 Planarity : 0.005 0.043 924 Dihedral : 6.859 76.906 753 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.89 % Allowed : 14.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.34), residues: 661 helix: 1.23 (0.27), residues: 382 sheet: -0.41 (0.71), residues: 48 loop : 0.99 (0.47), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.002 0.001 HIS A 370 PHE 0.015 0.002 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.004 0.000 ARG A 518 *********************** 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 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7602 (mp0) REVERT: A 373 LYS cc_start: 0.8383 (mppt) cc_final: 0.8123 (mmmm) REVERT: A 377 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: B 83 ASN cc_start: 0.8757 (m-40) cc_final: 0.8508 (m-40) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 2.2260 time to fit residues: 211.0738 Evaluate side-chains 89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 72 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5535 Z= 0.204 Angle : 0.504 5.008 7540 Z= 0.272 Chirality : 0.038 0.133 828 Planarity : 0.005 0.043 924 Dihedral : 6.856 74.989 753 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.34), residues: 661 helix: 1.33 (0.27), residues: 382 sheet: -0.33 (0.70), residues: 48 loop : 1.02 (0.47), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.003 0.001 HIS A 370 PHE 0.016 0.002 PHE A 316 TYR 0.014 0.001 TYR A 84 ARG 0.003 0.001 ARG A 518 *********************** 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 89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7615 (mp0) REVERT: A 373 LYS cc_start: 0.8296 (mppt) cc_final: 0.8059 (mmmm) REVERT: A 377 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: B 83 ASN cc_start: 0.8772 (m-40) cc_final: 0.8528 (m-40) outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 2.2942 time to fit residues: 209.9683 Evaluate side-chains 87 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5535 Z= 0.178 Angle : 0.487 5.027 7540 Z= 0.262 Chirality : 0.037 0.131 828 Planarity : 0.005 0.043 924 Dihedral : 6.598 74.069 751 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.43 % Allowed : 14.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.34), residues: 661 helix: 1.45 (0.27), residues: 382 sheet: -0.75 (0.72), residues: 42 loop : 1.01 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.002 0.001 HIS A 220 PHE 0.014 0.001 PHE A 316 TYR 0.014 0.001 TYR A 84 ARG 0.003 0.000 ARG A 518 *********************** 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 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7620 (mp0) REVERT: A 373 LYS cc_start: 0.8308 (mppt) cc_final: 0.8027 (mmmm) REVERT: A 377 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: B 83 ASN cc_start: 0.8765 (m-40) cc_final: 0.8550 (m-40) outliers start: 8 outliers final: 4 residues processed: 88 average time/residue: 2.2101 time to fit residues: 204.9198 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 : 0.892 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN B 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5535 Z= 0.198 Angle : 0.497 5.053 7540 Z= 0.267 Chirality : 0.037 0.132 828 Planarity : 0.005 0.043 924 Dihedral : 6.586 73.556 751 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.34), residues: 661 helix: 1.51 (0.27), residues: 378 sheet: -0.69 (0.70), residues: 42 loop : 0.94 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 PHE 0.015 0.001 PHE A 316 TYR 0.014 0.001 TYR A 391 ARG 0.003 0.000 ARG A 216 *********************** 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 88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7624 (mp0) REVERT: A 373 LYS cc_start: 0.8331 (mppt) cc_final: 0.8024 (mmmm) REVERT: A 377 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 421 MET cc_start: 0.8546 (mtm) cc_final: 0.8306 (mtm) REVERT: B 56 ILE cc_start: 0.8808 (mt) cc_final: 0.8591 (mp) REVERT: B 83 ASN cc_start: 0.8768 (m-40) cc_final: 0.8549 (m-40) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 2.3731 time to fit residues: 211.9949 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 : 0.888 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN B 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5535 Z= 0.161 Angle : 0.475 5.097 7540 Z= 0.254 Chirality : 0.037 0.131 828 Planarity : 0.005 0.042 924 Dihedral : 6.290 73.064 751 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.34), residues: 661 helix: 1.61 (0.27), residues: 378 sheet: -0.58 (0.69), residues: 42 loop : 0.94 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 PHE 0.012 0.001 PHE A 316 TYR 0.013 0.001 TYR A 84 ARG 0.002 0.000 ARG A 518 *********************** 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 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7624 (mp0) REVERT: A 373 LYS cc_start: 0.8287 (mppt) cc_final: 0.7964 (mmmm) REVERT: A 377 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 566 MET cc_start: 0.8608 (mtp) cc_final: 0.8390 (mtm) REVERT: B 56 ILE cc_start: 0.8814 (mt) cc_final: 0.8595 (mp) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 2.1630 time to fit residues: 201.7071 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 : 0.808 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5535 Z= 0.200 Angle : 0.493 5.052 7540 Z= 0.266 Chirality : 0.038 0.133 828 Planarity : 0.005 0.043 924 Dihedral : 6.333 72.807 751 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.89 % Allowed : 14.97 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.34), residues: 661 helix: 1.58 (0.27), residues: 378 sheet: -0.50 (0.69), residues: 42 loop : 0.96 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 PHE 0.016 0.002 PHE A 316 TYR 0.013 0.001 TYR A 84 ARG 0.003 0.000 ARG A 216 *********************** 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: 5 poor density : 80 time to evaluate : 0.776 Fit side-chains REVERT: A 304 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7639 (mp0) REVERT: A 377 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7929 (pm20) outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 2.4993 time to fit residues: 214.9871 Evaluate side-chains 83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5535 Z= 0.215 Angle : 0.497 5.092 7540 Z= 0.269 Chirality : 0.038 0.133 828 Planarity : 0.005 0.043 924 Dihedral : 6.368 72.329 751 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.71 % Allowed : 15.15 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.34), residues: 661 helix: 1.49 (0.27), residues: 382 sheet: -0.17 (0.71), residues: 40 loop : 0.96 (0.46), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 PHE 0.016 0.002 PHE A 316 TYR 0.014 0.001 TYR A 84 ARG 0.003 0.000 ARG A 216 *********************** 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 82 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.827 Fit side-chains REVERT: A 304 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7638 (mp0) REVERT: A 377 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7935 (pm20) outliers start: 4 outliers final: 3 residues processed: 80 average time/residue: 2.3749 time to fit residues: 199.7674 Evaluate side-chains 83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 7 optimal weight: 0.2980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 581 GLN A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5535 Z= 0.188 Angle : 0.487 5.167 7540 Z= 0.262 Chirality : 0.037 0.132 828 Planarity : 0.005 0.043 924 Dihedral : 6.266 71.831 751 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.71 % Allowed : 15.33 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.34), residues: 661 helix: 1.51 (0.27), residues: 382 sheet: -0.35 (0.70), residues: 42 loop : 0.98 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 PHE 0.014 0.001 PHE A 316 TYR 0.014 0.001 TYR A 84 ARG 0.002 0.000 ARG A 216 ********************** 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 84 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7638 (mp0) REVERT: A 377 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7972 (pm20) outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 2.3587 time to fit residues: 203.4503 Evaluate side-chains 83 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3706 r_free = 0.3706 target = 0.145063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120285 restraints weight = 22935.575| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.55 r_work: 0.3307 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5535 Z= 0.179 Angle : 0.485 5.193 7540 Z= 0.261 Chirality : 0.037 0.131 828 Planarity : 0.005 0.043 924 Dihedral : 6.166 71.224 751 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.89 % Allowed : 15.33 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.34), residues: 661 helix: 1.55 (0.27), residues: 382 sheet: -0.33 (0.71), residues: 42 loop : 1.02 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 556 HIS 0.002 0.001 HIS A 370 PHE 0.014 0.001 PHE A 316 TYR 0.014 0.001 TYR A 84 ARG 0.003 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5075.50 seconds wall clock time: 90 minutes 25.20 seconds (5425.20 seconds total)