Starting phenix.real_space_refine on Wed Jul 1 22:07:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6n_33644/07_2026/7y6n_33644.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.33 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: 0.29 Conformation dependent library (CDL) restraints added in 145.9 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: 0.10 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: 0.43 Time building geometry restraints manager: 0.38 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: 1782 16.24 - 32.47: 172 32.47 - 48.71: 30 48.71 - 64.94: 14 64.94 - 81.18: 3 Dihedral angle restraints: 2001 sinusoidal: 775 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 1998 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: 0.260 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.390 Find NCS groups from input model: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 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 : 13.038 81.022 1205 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (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 ARG 0.003 0.000 ARG H 19 TYR 0.009 0.001 TYR A 365 PHE 0.021 0.001 PHE L 92 TRP 0.026 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 3411) covalent geometry : angle 0.83660 / 0.44 ( 4635) SS BOND : bond 0.00496 / 0.23 ( 6) SS BOND : angle 2.78045 / 2.31 ( 12) hydrogen bonds : bond 0.15178 / 10.01 ( 100) hydrogen bonds : angle 8.66608 / 5.98 ( 228) link_NAG-ASN : bond 0.01563 / 0.82 ( 1) link_NAG-ASN : angle 4.67945 / 3.43 ( 3) *********************** 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 : 0.122 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: 0.5883 (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: 0.7297 (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: 0.0718 time to fit residues: 9.2091 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 : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.0000 overall best weight: 3.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.136558 restraints weight = 5758.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140082 restraints weight = 3741.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142595 restraints weight = 2701.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144116 restraints weight = 2112.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145349 restraints weight = 1779.819| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 3418 Z= 0.196 Angle : 0.833 7.869 4650 Z= 0.427 Chirality : 0.049 0.178 501 Planarity : 0.006 0.074 601 Dihedral : 5.916 27.062 470 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.40), residues: 420 helix: -2.01 (1.00), residues: 27 sheet: -1.68 (0.41), residues: 145 loop : -1.97 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 101 TYR 0.013 0.002 TYR A 505 PHE 0.015 0.002 PHE A 429 TRP 0.019 0.002 TRP L 35 HIS 0.004 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 3411) covalent geometry : angle 0.80395 / 0.42 ( 4635) SS BOND : bond 0.00728 / 0.36 ( 6) SS BOND : angle 3.77725 / 2.94 ( 12) hydrogen bonds : bond 0.03826 / 2.29 ( 100) hydrogen bonds : angle 7.38488 / 5.24 ( 228) link_NAG-ASN : bond 0.01550 / 0.82 ( 1) link_NAG-ASN : angle 4.59422 / 3.40 ( 3) *********************** 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 87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.6767 (tt) cc_final: 0.6276 (tp) REVERT: A 417 LYS cc_start: 0.7542 (ptmt) cc_final: 0.7110 (tppt) REVERT: A 436 TRP cc_start: 0.7254 (p90) cc_final: 0.6909 (p90) REVERT: A 439 ASN cc_start: 0.8136 (t0) cc_final: 0.7912 (t0) REVERT: A 453 TYR cc_start: 0.7677 (p90) cc_final: 0.7333 (p90) REVERT: H 29 PHE cc_start: 0.6109 (t80) cc_final: 0.5778 (t80) REVERT: H 78 SER cc_start: 0.6814 (t) cc_final: 0.6320 (m) REVERT: H 101 ARG cc_start: 0.7339 (tpt170) cc_final: 0.6293 (ttm170) REVERT: H 113 PHE cc_start: 0.7460 (m-80) cc_final: 0.7243 (m-80) REVERT: L 22 THR cc_start: 0.6356 (p) cc_final: 0.5999 (m) REVERT: L 92 PHE cc_start: 0.6176 (t80) cc_final: 0.5870 (t80) REVERT: L 102 THR cc_start: 0.6429 (t) cc_final: 0.5923 (m) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0574 time to fit residues: 6.2949 Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138938 restraints weight = 5813.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142523 restraints weight = 3739.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144990 restraints weight = 2679.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146739 restraints weight = 2090.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147874 restraints weight = 1736.638| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2763 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= 0.144 Angle : 0.764 7.165 4650 Z= 0.389 Chirality : 0.047 0.177 501 Planarity : 0.005 0.033 601 Dihedral : 5.765 25.653 470 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.41), residues: 420 helix: -2.10 (1.02), residues: 27 sheet: -1.78 (0.40), residues: 149 loop : -1.78 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.011 0.002 TYR L 49 PHE 0.014 0.001 PHE A 497 TRP 0.021 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3411) covalent geometry : angle 0.73725 / 0.38 ( 4635) SS BOND : bond 0.00396 / 0.17 ( 6) SS BOND : angle 3.41381 / 2.83 ( 12) hydrogen bonds : bond 0.03383 / 2.05 ( 100) hydrogen bonds : angle 7.19893 / 5.07 ( 228) link_NAG-ASN : bond 0.01380 / 0.73 ( 1) link_NAG-ASN : angle 4.35609 / 3.33 ( 3) *********************** 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 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7091 (mm) cc_final: 0.6817 (mt) REVERT: A 387 LEU cc_start: 0.6687 (tt) cc_final: 0.6414 (tp) REVERT: A 417 LYS cc_start: 0.7594 (ptmt) cc_final: 0.7146 (tppt) REVERT: A 462 LYS cc_start: 0.8349 (tppt) cc_final: 0.7587 (ptmt) REVERT: H 29 PHE cc_start: 0.6150 (t80) cc_final: 0.5704 (t80) REVERT: H 78 SER cc_start: 0.6674 (t) cc_final: 0.6323 (m) REVERT: H 93 LEU cc_start: 0.7088 (mt) cc_final: 0.6801 (mt) REVERT: H 101 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6161 (ttm170) REVERT: H 113 PHE cc_start: 0.7439 (m-80) cc_final: 0.7035 (m-80) REVERT: L 92 PHE cc_start: 0.6433 (t80) cc_final: 0.5789 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0674 time to fit residues: 7.0466 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 : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN L 34 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137963 restraints weight = 5928.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141255 restraints weight = 3878.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143575 restraints weight = 2836.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145093 restraints weight = 2236.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145948 restraints weight = 1883.618| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3418 Z= 0.213 Angle : 0.856 8.080 4650 Z= 0.440 Chirality : 0.050 0.214 501 Planarity : 0.005 0.032 601 Dihedral : 6.330 27.606 470 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.41), residues: 420 helix: -2.10 (1.05), residues: 27 sheet: -1.84 (0.39), residues: 149 loop : -1.89 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 403 TYR 0.017 0.003 TYR A 508 PHE 0.012 0.002 PHE A 497 TRP 0.030 0.003 TRP L 35 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 3411) covalent geometry : angle 0.82601 / 0.43 ( 4635) SS BOND : bond 0.00619 / 0.26 ( 6) SS BOND : angle 4.05961 / 3.28 ( 12) hydrogen bonds : bond 0.04036 / 2.43 ( 100) hydrogen bonds : angle 7.31439 / 5.11 ( 228) link_NAG-ASN : bond 0.01396 / 0.73 ( 1) link_NAG-ASN : angle 4.07544 / 3.22 ( 3) *********************** 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7613 (ptmt) cc_final: 0.7272 (tppt) REVERT: A 462 LYS cc_start: 0.8331 (tppt) cc_final: 0.7632 (ptmt) REVERT: H 13 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6574 (pm20) REVERT: H 72 ARG cc_start: 0.5642 (ttt90) cc_final: 0.5237 (ttt90) REVERT: H 78 SER cc_start: 0.6579 (t) cc_final: 0.6309 (m) REVERT: H 93 LEU cc_start: 0.7005 (mt) cc_final: 0.6650 (mt) REVERT: H 113 PHE cc_start: 0.7373 (m-80) cc_final: 0.6970 (m-80) REVERT: H 122 VAL cc_start: 0.5129 (t) cc_final: 0.4883 (t) REVERT: L 92 PHE cc_start: 0.6012 (t80) cc_final: 0.5280 (t80) REVERT: L 102 THR cc_start: 0.6342 (t) cc_final: 0.5863 (m) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0517 time to fit residues: 5.2381 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.0170 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.167008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141841 restraints weight = 5741.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145632 restraints weight = 3630.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148319 restraints weight = 2580.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150248 restraints weight = 1986.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151438 restraints weight = 1630.288| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3418 Z= 0.117 Angle : 0.733 6.716 4650 Z= 0.372 Chirality : 0.046 0.174 501 Planarity : 0.004 0.040 601 Dihedral : 5.614 25.137 470 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.41), residues: 420 helix: -2.07 (1.06), residues: 27 sheet: -1.57 (0.40), residues: 146 loop : -1.80 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 457 TYR 0.015 0.001 TYR A 453 PHE 0.016 0.002 PHE A 497 TRP 0.021 0.002 TRP H 114 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3411) covalent geometry : angle 0.71241 / 0.36 ( 4635) SS BOND : bond 0.00421 / 0.17 ( 6) SS BOND : angle 2.89331 / 2.34 ( 12) hydrogen bonds : bond 0.03083 / 1.85 ( 100) hydrogen bonds : angle 6.79785 / 4.79 ( 228) link_NAG-ASN : bond 0.01226 / 0.65 ( 1) link_NAG-ASN : angle 4.03346 / 3.28 ( 3) *********************** 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 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7213 (mm) cc_final: 0.6827 (mt) REVERT: A 393 THR cc_start: 0.6832 (m) cc_final: 0.6398 (p) REVERT: A 439 ASN cc_start: 0.8120 (t0) cc_final: 0.7748 (t0) REVERT: A 462 LYS cc_start: 0.8358 (tppt) cc_final: 0.7694 (ptmt) REVERT: H 13 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6574 (pm20) REVERT: H 101 ARG cc_start: 0.6906 (tpt90) cc_final: 0.6285 (ttp-170) REVERT: H 113 PHE cc_start: 0.7349 (m-80) cc_final: 0.7079 (m-80) REVERT: L 92 PHE cc_start: 0.5963 (t80) cc_final: 0.5175 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0679 time to fit residues: 6.7793 Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139136 restraints weight = 5919.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.142434 restraints weight = 3829.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144925 restraints weight = 2800.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146497 restraints weight = 2203.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147904 restraints weight = 1846.876| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3418 Z= 0.193 Angle : 0.856 8.481 4650 Z= 0.436 Chirality : 0.049 0.207 501 Planarity : 0.005 0.036 601 Dihedral : 6.263 27.307 470 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.41), residues: 420 helix: -2.39 (0.99), residues: 27 sheet: -1.80 (0.41), residues: 142 loop : -1.85 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.018 0.002 TYR A 453 PHE 0.019 0.002 PHE L 98 TRP 0.025 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 3411) covalent geometry : angle 0.82568 / 0.42 ( 4635) SS BOND : bond 0.00659 / 0.29 ( 6) SS BOND : angle 4.07393 / 3.27 ( 12) hydrogen bonds : bond 0.03962 / 2.37 ( 100) hydrogen bonds : angle 7.07800 / 4.95 ( 228) link_NAG-ASN : bond 0.01311 / 0.69 ( 1) link_NAG-ASN : angle 3.88524 / 3.17 ( 3) *********************** 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 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.6025 (mtm110) cc_final: 0.5375 (mtm110) REVERT: A 425 LEU cc_start: 0.8105 (mp) cc_final: 0.7821 (mp) REVERT: A 439 ASN cc_start: 0.8177 (t0) cc_final: 0.7797 (t0) REVERT: A 461 LEU cc_start: 0.6621 (mm) cc_final: 0.6246 (mm) REVERT: A 462 LYS cc_start: 0.8399 (tppt) cc_final: 0.7965 (pttm) REVERT: H 13 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6548 (pm20) REVERT: L 92 PHE cc_start: 0.6098 (t80) cc_final: 0.5116 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0656 time to fit residues: 6.6555 Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141579 restraints weight = 5903.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144990 restraints weight = 3833.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147506 restraints weight = 2746.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149335 restraints weight = 2138.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150367 restraints weight = 1758.591| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.4418 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= 0.142 Angle : 0.807 8.938 4650 Z= 0.408 Chirality : 0.048 0.187 501 Planarity : 0.005 0.039 601 Dihedral : 6.023 26.285 470 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.41), residues: 420 helix: -2.39 (0.98), residues: 27 sheet: -1.62 (0.41), residues: 147 loop : -1.83 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.024 0.002 TYR A 453 PHE 0.017 0.002 PHE A 497 TRP 0.028 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3411) covalent geometry : angle 0.78219 / 0.40 ( 4635) SS BOND : bond 0.00542 / 0.24 ( 6) SS BOND : angle 3.50180 / 2.82 ( 12) hydrogen bonds : bond 0.03585 / 2.09 ( 100) hydrogen bonds : angle 7.09574 / 4.96 ( 228) link_NAG-ASN : bond 0.01175 / 0.62 ( 1) link_NAG-ASN : angle 3.93790 / 3.26 ( 3) *********************** 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7305 (mm) cc_final: 0.6856 (mt) REVERT: A 393 THR cc_start: 0.6785 (m) cc_final: 0.6374 (p) REVERT: A 403 ARG cc_start: 0.5637 (mtm110) cc_final: 0.5288 (mtm110) REVERT: A 425 LEU cc_start: 0.8077 (mp) cc_final: 0.7727 (mp) REVERT: A 439 ASN cc_start: 0.8110 (t0) cc_final: 0.7777 (t0) REVERT: A 453 TYR cc_start: 0.6729 (p90) cc_final: 0.5440 (p90) REVERT: A 461 LEU cc_start: 0.6623 (mm) cc_final: 0.6273 (mm) REVERT: A 462 LYS cc_start: 0.8429 (tppt) cc_final: 0.8006 (pttm) REVERT: H 13 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6642 (pm20) REVERT: H 101 ARG cc_start: 0.7229 (tpt90) cc_final: 0.6298 (ttp-170) REVERT: H 113 PHE cc_start: 0.7222 (m-80) cc_final: 0.6969 (m-80) REVERT: L 37 GLN cc_start: 0.5895 (pp30) cc_final: 0.5567 (pp30) REVERT: L 92 PHE cc_start: 0.5960 (t80) cc_final: 0.5451 (t80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0562 time to fit residues: 5.8615 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0670 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 GLN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.171136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146265 restraints weight = 5839.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149802 restraints weight = 3782.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152162 restraints weight = 2727.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154007 restraints weight = 2143.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155493 restraints weight = 1783.256| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3418 Z= 0.124 Angle : 0.734 6.590 4650 Z= 0.372 Chirality : 0.045 0.190 501 Planarity : 0.004 0.039 601 Dihedral : 5.517 25.139 470 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.42), residues: 420 helix: -2.31 (1.02), residues: 27 sheet: -1.30 (0.42), residues: 140 loop : -1.79 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.012 0.001 TYR A 453 PHE 0.012 0.002 PHE L 62 TRP 0.023 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3411) covalent geometry : angle 0.71227 / 0.36 ( 4635) SS BOND : bond 0.00745 / 0.33 ( 6) SS BOND : angle 2.98338 / 2.41 ( 12) hydrogen bonds : bond 0.03188 / 1.95 ( 100) hydrogen bonds : angle 6.75937 / 4.70 ( 228) link_NAG-ASN : bond 0.01289 / 0.68 ( 1) link_NAG-ASN : angle 4.05110 / 3.41 ( 3) *********************** 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7328 (mm) cc_final: 0.6909 (mt) REVERT: A 393 THR cc_start: 0.6627 (m) cc_final: 0.6253 (p) REVERT: A 425 LEU cc_start: 0.7953 (mp) cc_final: 0.7713 (mp) REVERT: A 461 LEU cc_start: 0.6773 (mm) cc_final: 0.6486 (mm) REVERT: A 462 LYS cc_start: 0.8390 (tppt) cc_final: 0.7998 (pttm) REVERT: H 13 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6599 (pm20) REVERT: H 72 ARG cc_start: 0.5258 (tpt-90) cc_final: 0.4955 (tpt-90) REVERT: H 101 ARG cc_start: 0.6857 (tpt90) cc_final: 0.5958 (ttp-170) REVERT: L 37 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.5681 (pp30) REVERT: L 92 PHE cc_start: 0.6323 (t80) cc_final: 0.5432 (t80) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0576 time to fit residues: 6.1562 Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 394 ASN L 34 ASN L 37 GLN L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144506 restraints weight = 5750.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147986 restraints weight = 3732.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150470 restraints weight = 2686.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152388 restraints weight = 2087.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153611 restraints weight = 1716.458| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3418 Z= 0.133 Angle : 0.767 7.545 4650 Z= 0.385 Chirality : 0.046 0.157 501 Planarity : 0.005 0.037 601 Dihedral : 5.745 25.274 470 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.42), residues: 420 helix: -2.27 (1.04), residues: 27 sheet: -1.38 (0.43), residues: 141 loop : -1.70 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.016 0.001 TYR A 453 PHE 0.011 0.002 PHE A 429 TRP 0.027 0.002 TRP L 35 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3411) covalent geometry : angle 0.74255 / 0.38 ( 4635) SS BOND : bond 0.00500 / 0.21 ( 6) SS BOND : angle 3.23854 / 2.70 ( 12) hydrogen bonds : bond 0.03265 / 1.94 ( 100) hydrogen bonds : angle 6.77714 / 4.71 ( 228) link_NAG-ASN : bond 0.01175 / 0.62 ( 1) link_NAG-ASN : angle 4.12628 / 3.40 ( 3) *********************** 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 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7362 (mm) cc_final: 0.6927 (mt) REVERT: A 393 THR cc_start: 0.6670 (m) cc_final: 0.6301 (p) REVERT: A 403 ARG cc_start: 0.5776 (mtm110) cc_final: 0.5373 (mtm110) REVERT: A 425 LEU cc_start: 0.8058 (mp) cc_final: 0.7789 (mp) REVERT: A 462 LYS cc_start: 0.8413 (tppt) cc_final: 0.7776 (ptmt) REVERT: H 13 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6575 (pm20) REVERT: H 72 ARG cc_start: 0.5549 (tpt-90) cc_final: 0.5185 (tpt-90) REVERT: H 101 ARG cc_start: 0.7112 (tpt90) cc_final: 0.6232 (ttp-170) REVERT: L 92 PHE cc_start: 0.6357 (t80) cc_final: 0.5464 (t80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0612 time to fit residues: 6.0859 Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3928 r_free = 0.3928 target = 0.166372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142455 restraints weight = 5782.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145750 restraints weight = 3743.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148174 restraints weight = 2701.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149690 restraints weight = 2111.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150930 restraints weight = 1771.071| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3418 Z= 0.167 Angle : 0.805 7.385 4650 Z= 0.408 Chirality : 0.048 0.169 501 Planarity : 0.005 0.035 601 Dihedral : 6.042 26.650 470 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.42), residues: 420 helix: -3.01 (0.81), residues: 33 sheet: -1.33 (0.43), residues: 135 loop : -1.91 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.023 0.002 TYR A 453 PHE 0.012 0.002 PHE A 497 TRP 0.034 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 3411) covalent geometry : angle 0.78109 / 0.40 ( 4635) SS BOND : bond 0.00461 / 0.19 ( 6) SS BOND : angle 3.40840 / 2.80 ( 12) hydrogen bonds : bond 0.03547 / 2.14 ( 100) hydrogen bonds : angle 7.00216 / 4.86 ( 228) link_NAG-ASN : bond 0.01171 / 0.62 ( 1) link_NAG-ASN : angle 3.78654 / 3.15 ( 3) ********************** 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 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7442 (mm) cc_final: 0.6953 (mt) REVERT: A 462 LYS cc_start: 0.8483 (tppt) cc_final: 0.7800 (ptmt) REVERT: H 13 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6459 (pm20) REVERT: H 104 TRP cc_start: 0.5057 (t60) cc_final: 0.4846 (t60) REVERT: L 92 PHE cc_start: 0.6300 (t80) cc_final: 0.5389 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0630 time to fit residues: 6.4337 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 : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143170 restraints weight = 5879.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146692 restraints weight = 3774.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149329 restraints weight = 2723.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151221 restraints weight = 2116.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152522 restraints weight = 1739.098| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3418 Z= 0.131 Angle : 0.760 7.085 4650 Z= 0.384 Chirality : 0.046 0.156 501 Planarity : 0.005 0.036 601 Dihedral : 5.842 25.841 470 Min Nonbonded Distance : 2.561 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.42), residues: 420 helix: -2.57 (0.95), residues: 27 sheet: -1.44 (0.42), residues: 141 loop : -1.75 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 408 TYR 0.014 0.002 TYR A 508 PHE 0.012 0.002 PHE H 111 TRP 0.032 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3411) covalent geometry : angle 0.73843 / 0.38 ( 4635) SS BOND : bond 0.00542 / 0.24 ( 6) SS BOND : angle 3.11964 / 2.56 ( 12) hydrogen bonds : bond 0.03261 / 1.94 ( 100) hydrogen bonds : angle 6.83653 / 4.77 ( 228) link_NAG-ASN : bond 0.01142 / 0.60 ( 1) link_NAG-ASN : angle 3.85832 / 3.24 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 758.39 seconds wall clock time: 13 minutes 46.24 seconds (826.24 seconds total)