Starting phenix.real_space_refine on Wed Jul 23 12:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6n_33644/07_2025/7y6n_33644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6n_33644/07_2025/7y6n_33644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2025/7y6n_33644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2025/7y6n_33644.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2025/7y6n_33644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2025/7y6n_33644.cif" } resolution = 4.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2112 2.51 5 N 565 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3327 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.95, per 1000 atoms: 0.89 Number of scatterers: 3327 At special positions: 0 Unit cell: (65.491, 60.517, 107.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 635 8.00 N 565 7.00 C 2112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 451.7 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.9% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.916A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.965A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.909A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.933A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.496A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY H 50 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.500A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 228 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: 0.89 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1069 1.34 - 1.47: 901 1.47 - 1.59: 1424 1.59 - 1.71: 0 1.71 - 1.83: 17 Bond restraints: 3411 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" CB LYS A 462 " pdb=" CG LYS A 462 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" N ASN H 77 " pdb=" CA ASN H 77 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 4365 1.54 - 3.09: 214 3.09 - 4.63: 38 4.63 - 6.18: 10 6.18 - 7.72: 8 Bond angle restraints: 4635 Sorted by residual: angle pdb=" C PRO A 479 " pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta sigma weight residual 121.94 114.95 6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 114.56 110.18 4.38 1.27e+00 6.20e-01 1.19e+01 angle pdb=" CB LYS A 462 " pdb=" CG LYS A 462 " pdb=" CD LYS A 462 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" N GLY L 41 " pdb=" CA GLY L 41 " pdb=" C GLY L 41 " ideal model delta sigma weight residual 113.58 116.85 -3.27 1.07e+00 8.73e-01 9.33e+00 angle pdb=" N PHE L 92 " pdb=" CA PHE L 92 " pdb=" C PHE L 92 " ideal model delta sigma weight residual 109.96 105.46 4.50 1.58e+00 4.01e-01 8.10e+00 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1799 16.24 - 32.47: 176 32.47 - 48.71: 30 48.71 - 64.94: 14 64.94 - 81.18: 3 Dihedral angle restraints: 2022 sinusoidal: 796 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 11.82 81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.64 -62.64 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -147.95 61.95 1 1.00e+01 1.00e-02 5.09e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 356 0.046 - 0.091: 106 0.091 - 0.137: 34 0.137 - 0.182: 4 0.182 - 0.228: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 498 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.070 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 491 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.012 2.00e-02 2.50e+03 9.63e-03 2.32e+00 pdb=" CG TRP H 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO L 59 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.018 5.00e-02 4.00e+02 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 507 2.76 - 3.29: 3418 3.29 - 3.83: 5417 3.83 - 4.36: 6147 4.36 - 4.90: 10455 Nonbonded interactions: 25944 Sorted by model distance: nonbonded pdb=" O GLY H 85 " pdb=" NH1 ARG H 87 " model vdw 2.222 3.120 nonbonded pdb=" OG SER L 14 " pdb=" O LYS L 107 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR H 102 " pdb=" NE2 GLN L 55 " model vdw 2.266 3.120 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASN A 354 " pdb=" N ARG A 355 " model vdw 2.302 3.120 ... (remaining 25939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 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 : 0.003 0.035 3418 Z= 0.157 Angle : 0.855 7.724 4650 Z= 0.449 Chirality : 0.047 0.228 501 Planarity : 0.006 0.108 601 Dihedral : 12.983 81.022 1226 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.39), residues: 420 helix: -2.48 (0.92), residues: 28 sheet: -1.35 (0.43), residues: 138 loop : -2.10 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.021 0.001 PHE L 92 TYR 0.009 0.001 TYR A 365 ARG 0.003 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01563 ( 1) link_NAG-ASN : angle 4.67945 ( 3) hydrogen bonds : bond 0.15178 ( 100) hydrogen bonds : angle 8.66608 ( 228) SS BOND : bond 0.00496 ( 6) SS BOND : angle 2.78045 ( 12) covalent geometry : bond 0.00324 ( 3411) covalent geometry : angle 0.83660 ( 4635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.5807 (tt) cc_final: 0.5411 (tp) REVERT: A 417 LYS cc_start: 0.6909 (ptmt) cc_final: 0.6335 (tppt) REVERT: A 424 LYS cc_start: 0.7203 (tmmt) cc_final: 0.6589 (tptt) REVERT: A 436 TRP cc_start: 0.6532 (p90) cc_final: 0.5933 (p90) REVERT: A 439 ASN cc_start: 0.6843 (t0) cc_final: 0.6558 (t0) REVERT: A 453 TYR cc_start: 0.6462 (p90) cc_final: 0.5882 (p90) REVERT: A 461 LEU cc_start: 0.6388 (mm) cc_final: 0.6047 (mm) REVERT: A 466 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7368 (ttm170) REVERT: A 489 TYR cc_start: 0.7858 (m-10) cc_final: 0.7087 (m-10) REVERT: H 78 SER cc_start: 0.7214 (t) cc_final: 0.6535 (m) REVERT: H 90 ASP cc_start: 0.4947 (m-30) cc_final: 0.4626 (m-30) REVERT: H 101 ARG cc_start: 0.7298 (tpt170) cc_final: 0.5685 (ttm170) REVERT: L 92 PHE cc_start: 0.5994 (t80) cc_final: 0.5333 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1626 time to fit residues: 20.6114 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137152 restraints weight = 5701.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140734 restraints weight = 3684.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143073 restraints weight = 2655.564| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3418 Z= 0.177 Angle : 0.812 7.365 4650 Z= 0.418 Chirality : 0.048 0.176 501 Planarity : 0.006 0.073 601 Dihedral : 6.333 28.259 491 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.40), residues: 420 helix: -2.16 (0.96), residues: 27 sheet: -1.67 (0.40), residues: 150 loop : -1.93 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.004 0.003 HIS H 35 PHE 0.015 0.002 PHE A 497 TYR 0.013 0.002 TYR L 49 ARG 0.004 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01570 ( 1) link_NAG-ASN : angle 4.53630 ( 3) hydrogen bonds : bond 0.03751 ( 100) hydrogen bonds : angle 7.27313 ( 228) SS BOND : bond 0.00711 ( 6) SS BOND : angle 3.47558 ( 12) covalent geometry : bond 0.00404 ( 3411) covalent geometry : angle 0.78580 ( 4635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.6773 (tt) cc_final: 0.6266 (tp) REVERT: A 417 LYS cc_start: 0.7536 (ptmt) cc_final: 0.7100 (tppt) REVERT: A 436 TRP cc_start: 0.7239 (p90) cc_final: 0.6916 (p90) REVERT: A 453 TYR cc_start: 0.7618 (p90) cc_final: 0.7350 (p90) REVERT: H 34 MET cc_start: 0.6267 (tpt) cc_final: 0.6039 (tpt) REVERT: H 72 ARG cc_start: 0.5557 (ttt90) cc_final: 0.5164 (tpt-90) REVERT: H 78 SER cc_start: 0.6875 (t) cc_final: 0.6502 (m) REVERT: H 101 ARG cc_start: 0.7297 (tpt170) cc_final: 0.6388 (ttm170) REVERT: L 22 THR cc_start: 0.6401 (p) cc_final: 0.6081 (m) REVERT: L 92 PHE cc_start: 0.6257 (t80) cc_final: 0.5630 (t80) REVERT: L 102 THR cc_start: 0.6357 (t) cc_final: 0.5854 (m) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1552 time to fit residues: 15.8425 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136256 restraints weight = 5758.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139409 restraints weight = 3781.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141638 restraints weight = 2771.109| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3418 Z= 0.211 Angle : 0.850 7.907 4650 Z= 0.438 Chirality : 0.049 0.182 501 Planarity : 0.006 0.043 601 Dihedral : 6.959 39.102 491 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.41), residues: 420 helix: -2.26 (0.99), residues: 27 sheet: -1.87 (0.40), residues: 145 loop : -1.93 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP L 35 HIS 0.004 0.003 HIS A 519 PHE 0.015 0.002 PHE A 497 TYR 0.015 0.002 TYR L 49 ARG 0.005 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01512 ( 1) link_NAG-ASN : angle 4.36384 ( 3) hydrogen bonds : bond 0.03947 ( 100) hydrogen bonds : angle 7.54430 ( 228) SS BOND : bond 0.00509 ( 6) SS BOND : angle 3.94672 ( 12) covalent geometry : bond 0.00481 ( 3411) covalent geometry : angle 0.81977 ( 4635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7136 (mm) cc_final: 0.6712 (mt) REVERT: A 387 LEU cc_start: 0.6789 (tt) cc_final: 0.6509 (tp) REVERT: A 417 LYS cc_start: 0.7665 (ptmt) cc_final: 0.7179 (tppt) REVERT: A 439 ASN cc_start: 0.8086 (t0) cc_final: 0.7834 (t0) REVERT: H 13 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6562 (pm20) REVERT: H 29 PHE cc_start: 0.6231 (t80) cc_final: 0.5867 (t80) REVERT: H 78 SER cc_start: 0.6607 (t) cc_final: 0.6383 (m) REVERT: H 93 LEU cc_start: 0.7006 (mt) cc_final: 0.6631 (mt) REVERT: H 101 ARG cc_start: 0.7374 (tpt90) cc_final: 0.6542 (ttp-170) REVERT: L 92 PHE cc_start: 0.6231 (t80) cc_final: 0.5542 (t80) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1603 time to fit residues: 16.3368 Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136907 restraints weight = 5887.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140261 restraints weight = 3779.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142671 restraints weight = 2734.208| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3418 Z= 0.189 Angle : 0.833 7.422 4650 Z= 0.430 Chirality : 0.049 0.181 501 Planarity : 0.005 0.042 601 Dihedral : 6.996 38.143 491 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.41), residues: 420 helix: -2.64 (0.91), residues: 27 sheet: -1.87 (0.40), residues: 148 loop : -1.88 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.014 0.002 PHE A 497 TYR 0.016 0.002 TYR A 453 ARG 0.005 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01331 ( 1) link_NAG-ASN : angle 4.22393 ( 3) hydrogen bonds : bond 0.03730 ( 100) hydrogen bonds : angle 7.42945 ( 228) SS BOND : bond 0.00533 ( 6) SS BOND : angle 3.93719 ( 12) covalent geometry : bond 0.00428 ( 3411) covalent geometry : angle 0.80308 ( 4635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7279 (mm) cc_final: 0.6833 (mt) REVERT: A 417 LYS cc_start: 0.7692 (ptmt) cc_final: 0.7345 (tppt) REVERT: A 439 ASN cc_start: 0.8224 (t0) cc_final: 0.7844 (t0) REVERT: A 461 LEU cc_start: 0.6524 (mm) cc_final: 0.6039 (mm) REVERT: A 462 LYS cc_start: 0.8366 (tppt) cc_final: 0.7961 (pttm) REVERT: H 13 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6567 (pm20) REVERT: H 29 PHE cc_start: 0.6270 (t80) cc_final: 0.5750 (t80) REVERT: H 122 VAL cc_start: 0.5206 (t) cc_final: 0.4952 (t) REVERT: L 71 PHE cc_start: 0.6855 (m-80) cc_final: 0.5882 (m-80) REVERT: L 92 PHE cc_start: 0.6097 (t80) cc_final: 0.5369 (t80) REVERT: L 102 THR cc_start: 0.6219 (t) cc_final: 0.5708 (m) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1689 time to fit residues: 16.8561 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138451 restraints weight = 5811.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141888 restraints weight = 3703.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144345 restraints weight = 2662.614| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3418 Z= 0.153 Angle : 0.783 6.926 4650 Z= 0.403 Chirality : 0.048 0.174 501 Planarity : 0.005 0.037 601 Dihedral : 6.538 30.827 491 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.41), residues: 420 helix: -2.65 (0.92), residues: 27 sheet: -1.78 (0.40), residues: 147 loop : -1.88 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.002 PHE A 515 TYR 0.015 0.002 TYR A 453 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.01320 ( 1) link_NAG-ASN : angle 4.19970 ( 3) hydrogen bonds : bond 0.03528 ( 100) hydrogen bonds : angle 7.10242 ( 228) SS BOND : bond 0.00483 ( 6) SS BOND : angle 3.51661 ( 12) covalent geometry : bond 0.00344 ( 3411) covalent geometry : angle 0.75601 ( 4635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7243 (mm) cc_final: 0.6803 (mt) REVERT: A 417 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7411 (tppt) REVERT: A 439 ASN cc_start: 0.8185 (t0) cc_final: 0.7791 (t0) REVERT: A 461 LEU cc_start: 0.6586 (mm) cc_final: 0.6182 (mm) REVERT: A 462 LYS cc_start: 0.8374 (tppt) cc_final: 0.7961 (pttm) REVERT: H 13 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6566 (pm20) REVERT: H 122 VAL cc_start: 0.5301 (t) cc_final: 0.5051 (t) REVERT: L 92 PHE cc_start: 0.6080 (t80) cc_final: 0.5208 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1601 time to fit residues: 15.7947 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.0030 chunk 34 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143970 restraints weight = 5837.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147490 restraints weight = 3629.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150027 restraints weight = 2594.764| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3418 Z= 0.119 Angle : 0.736 8.136 4650 Z= 0.375 Chirality : 0.046 0.199 501 Planarity : 0.005 0.044 601 Dihedral : 5.872 25.722 491 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.41), residues: 420 helix: -2.53 (0.97), residues: 27 sheet: -1.78 (0.40), residues: 148 loop : -1.83 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 114 HIS 0.001 0.001 HIS H 35 PHE 0.019 0.002 PHE A 429 TYR 0.014 0.001 TYR A 453 ARG 0.003 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.01330 ( 1) link_NAG-ASN : angle 4.36021 ( 3) hydrogen bonds : bond 0.03054 ( 100) hydrogen bonds : angle 6.75525 ( 228) SS BOND : bond 0.00523 ( 6) SS BOND : angle 2.80414 ( 12) covalent geometry : bond 0.00255 ( 3411) covalent geometry : angle 0.71431 ( 4635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7244 (mm) cc_final: 0.6835 (mt) REVERT: A 393 THR cc_start: 0.6642 (m) cc_final: 0.6223 (p) REVERT: A 439 ASN cc_start: 0.8104 (t0) cc_final: 0.7776 (t0) REVERT: A 461 LEU cc_start: 0.6584 (mm) cc_final: 0.6179 (mm) REVERT: A 462 LYS cc_start: 0.8352 (tppt) cc_final: 0.7972 (pttm) REVERT: H 13 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6629 (pm20) REVERT: H 101 ARG cc_start: 0.6882 (tpt90) cc_final: 0.6212 (ttp-170) REVERT: L 37 GLN cc_start: 0.5995 (pp30) cc_final: 0.5625 (pp30) REVERT: L 92 PHE cc_start: 0.6044 (t80) cc_final: 0.5147 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1671 time to fit residues: 17.1635 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 394 ASN L 34 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.170520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145989 restraints weight = 5773.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149630 restraints weight = 3706.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152167 restraints weight = 2646.080| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3418 Z= 0.113 Angle : 0.718 6.743 4650 Z= 0.362 Chirality : 0.045 0.199 501 Planarity : 0.004 0.040 601 Dihedral : 5.615 25.001 491 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.42), residues: 420 helix: -2.40 (0.99), residues: 27 sheet: -1.51 (0.42), residues: 146 loop : -1.72 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.036 0.002 PHE H 29 TYR 0.014 0.001 TYR A 453 ARG 0.004 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.01355 ( 1) link_NAG-ASN : angle 4.45322 ( 3) hydrogen bonds : bond 0.03008 ( 100) hydrogen bonds : angle 6.65920 ( 228) SS BOND : bond 0.00444 ( 6) SS BOND : angle 2.71453 ( 12) covalent geometry : bond 0.00239 ( 3411) covalent geometry : angle 0.69697 ( 4635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7236 (mm) cc_final: 0.6842 (mt) REVERT: A 386 LYS cc_start: 0.5428 (pptt) cc_final: 0.4846 (ptmt) REVERT: A 393 THR cc_start: 0.6590 (m) cc_final: 0.6222 (p) REVERT: A 461 LEU cc_start: 0.6551 (mm) cc_final: 0.6207 (mm) REVERT: A 462 LYS cc_start: 0.8390 (tppt) cc_final: 0.7954 (pttm) REVERT: H 13 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6589 (pm20) REVERT: H 101 ARG cc_start: 0.6864 (tpt90) cc_final: 0.6136 (ttp-170) REVERT: L 37 GLN cc_start: 0.6019 (pp30) cc_final: 0.5644 (pp30) REVERT: L 92 PHE cc_start: 0.6080 (t80) cc_final: 0.5145 (t80) REVERT: L 93 THR cc_start: 0.6997 (p) cc_final: 0.6772 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1524 time to fit residues: 14.4906 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.170765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146489 restraints weight = 5794.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150055 restraints weight = 3698.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152393 restraints weight = 2643.263| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3418 Z= 0.118 Angle : 0.732 7.734 4650 Z= 0.370 Chirality : 0.046 0.190 501 Planarity : 0.004 0.037 601 Dihedral : 5.751 24.846 491 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.42), residues: 420 helix: -2.37 (1.00), residues: 27 sheet: -1.33 (0.43), residues: 148 loop : -1.68 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 35 HIS 0.001 0.000 HIS H 35 PHE 0.014 0.002 PHE L 71 TYR 0.015 0.001 TYR A 453 ARG 0.003 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.01304 ( 1) link_NAG-ASN : angle 4.42733 ( 3) hydrogen bonds : bond 0.03242 ( 100) hydrogen bonds : angle 6.73542 ( 228) SS BOND : bond 0.00514 ( 6) SS BOND : angle 2.89758 ( 12) covalent geometry : bond 0.00254 ( 3411) covalent geometry : angle 0.70957 ( 4635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7236 (mm) cc_final: 0.6828 (mt) REVERT: A 386 LYS cc_start: 0.5512 (pptt) cc_final: 0.4679 (ptmt) REVERT: A 393 THR cc_start: 0.6601 (m) cc_final: 0.6223 (p) REVERT: A 425 LEU cc_start: 0.8095 (mp) cc_final: 0.7842 (mp) REVERT: A 461 LEU cc_start: 0.6466 (mm) cc_final: 0.6107 (mm) REVERT: A 462 LYS cc_start: 0.8413 (tppt) cc_final: 0.7975 (pttm) REVERT: H 13 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6578 (pm20) REVERT: H 101 ARG cc_start: 0.6826 (tpt90) cc_final: 0.6141 (ttp-170) REVERT: L 92 PHE cc_start: 0.6196 (t80) cc_final: 0.5450 (t80) REVERT: L 93 THR cc_start: 0.6925 (p) cc_final: 0.6591 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2103 time to fit residues: 20.6908 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142220 restraints weight = 5847.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145608 restraints weight = 3755.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148125 restraints weight = 2714.283| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3418 Z= 0.188 Angle : 0.837 7.886 4650 Z= 0.427 Chirality : 0.050 0.194 501 Planarity : 0.005 0.034 601 Dihedral : 6.646 28.088 491 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.42), residues: 420 helix: -2.53 (0.94), residues: 27 sheet: -1.53 (0.44), residues: 141 loop : -1.86 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.011 0.002 PHE A 497 TYR 0.023 0.002 TYR A 453 ARG 0.006 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01432 ( 1) link_NAG-ASN : angle 3.87639 ( 3) hydrogen bonds : bond 0.03740 ( 100) hydrogen bonds : angle 7.12172 ( 228) SS BOND : bond 0.00807 ( 6) SS BOND : angle 3.69945 ( 12) covalent geometry : bond 0.00429 ( 3411) covalent geometry : angle 0.81139 ( 4635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7344 (mm) cc_final: 0.6850 (mt) REVERT: A 461 LEU cc_start: 0.6406 (mm) cc_final: 0.5988 (mm) REVERT: A 462 LYS cc_start: 0.8417 (tppt) cc_final: 0.8006 (pttm) REVERT: H 13 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6540 (pm20) REVERT: H 104 TRP cc_start: 0.5033 (t60) cc_final: 0.4761 (t60) REVERT: H 122 VAL cc_start: 0.5457 (t) cc_final: 0.5235 (t) REVERT: L 22 THR cc_start: 0.6211 (p) cc_final: 0.5848 (m) REVERT: L 34 ASN cc_start: 0.7556 (m-40) cc_final: 0.7270 (m110) REVERT: L 92 PHE cc_start: 0.6351 (t80) cc_final: 0.5616 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1319 time to fit residues: 12.8456 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.167549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143234 restraints weight = 5692.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146788 restraints weight = 3601.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149398 restraints weight = 2563.468| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3418 Z= 0.154 Angle : 0.812 9.006 4650 Z= 0.409 Chirality : 0.048 0.170 501 Planarity : 0.005 0.033 601 Dihedral : 6.418 28.203 491 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.42), residues: 420 helix: -2.55 (0.93), residues: 27 sheet: -1.58 (0.43), residues: 143 loop : -1.90 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.024 0.002 PHE A 497 TYR 0.015 0.002 TYR A 453 ARG 0.003 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01258 ( 1) link_NAG-ASN : angle 4.00697 ( 3) hydrogen bonds : bond 0.03442 ( 100) hydrogen bonds : angle 6.97595 ( 228) SS BOND : bond 0.00499 ( 6) SS BOND : angle 3.74828 ( 12) covalent geometry : bond 0.00348 ( 3411) covalent geometry : angle 0.78366 ( 4635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.6426 (mm) cc_final: 0.6009 (mm) REVERT: A 462 LYS cc_start: 0.8383 (tppt) cc_final: 0.7969 (pttm) REVERT: H 13 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6374 (mm-40) REVERT: H 101 ARG cc_start: 0.6997 (tpt90) cc_final: 0.6136 (ttp-170) REVERT: H 104 TRP cc_start: 0.5038 (t60) cc_final: 0.4772 (t60) REVERT: L 92 PHE cc_start: 0.6445 (t80) cc_final: 0.5619 (t80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3594 time to fit residues: 33.1543 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.167040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143147 restraints weight = 5694.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146710 restraints weight = 3597.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149268 restraints weight = 2554.826| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3418 Z= 0.169 Angle : 0.831 8.753 4650 Z= 0.420 Chirality : 0.049 0.176 501 Planarity : 0.005 0.032 601 Dihedral : 6.591 27.878 491 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.41), residues: 420 helix: -2.59 (0.93), residues: 26 sheet: -1.57 (0.43), residues: 139 loop : -1.97 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.002 PHE A 497 TYR 0.028 0.002 TYR A 453 ARG 0.004 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01359 ( 1) link_NAG-ASN : angle 3.79287 ( 3) hydrogen bonds : bond 0.03538 ( 100) hydrogen bonds : angle 7.10883 ( 228) SS BOND : bond 0.00596 ( 6) SS BOND : angle 4.12275 ( 12) covalent geometry : bond 0.00384 ( 3411) covalent geometry : angle 0.80011 ( 4635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.14 seconds wall clock time: 33 minutes 56.22 seconds (2036.22 seconds total)