Starting phenix.real_space_refine on Tue Mar 3 14:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8z_33061/03_2026/7x8z_33061_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8z_33061/03_2026/7x8z_33061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2026/7x8z_33061_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2026/7x8z_33061_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2026/7x8z_33061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2026/7x8z_33061.map" } resolution = 4.1 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= 0.002 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: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2114 2.51 5 N 555 2.21 5 O 647 1.98 5 H 3147 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6480 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1789 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1689 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} 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: 1.19, per 1000 atoms: 0.18 Number of scatterers: 6480 At special positions: 0 Unit cell: (82.071, 84.558, 75.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 647 8.00 N 555 7.00 C 2114 6.00 H 3147 1.00 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=2.03 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 94 " 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: 0.44 Conformation dependent library (CDL) restraints added in 272.2 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: 772 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 8.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.623A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.077A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.950A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.950A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.459A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.852A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.588A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.780A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.580A pdb=" N THR L 59 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS L 96 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 103 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.580A pdb=" N THR L 59 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 207 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: 1.18 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3146 1.03 - 1.23: 3 1.23 - 1.42: 1529 1.42 - 1.62: 1867 1.62 - 1.81: 21 Bond restraints: 6566 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" N GLU H 1 " pdb=" H GLU H 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 6561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 10795 1.00 - 1.99: 866 1.99 - 2.99: 75 2.99 - 3.98: 14 3.98 - 4.98: 5 Bond angle restraints: 11755 Sorted by residual: angle pdb=" C TRP L 56 " pdb=" N ALA L 57 " pdb=" CA ALA L 57 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.74e+00 angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 106.55 109.94 -3.39 1.45e+00 4.76e-01 5.48e+00 angle pdb=" CA VAL H 48 " pdb=" C VAL H 48 " pdb=" N SER H 49 " ideal model delta sigma weight residual 116.60 119.90 -3.30 1.45e+00 4.76e-01 5.18e+00 angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 109.34 114.00 -4.66 2.08e+00 2.31e-01 5.01e+00 angle pdb=" N PRO L 101 " pdb=" CA PRO L 101 " pdb=" C PRO L 101 " ideal model delta sigma weight residual 110.70 112.76 -2.06 1.22e+00 6.72e-01 2.84e+00 ... (remaining 11750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2789 15.96 - 31.92: 272 31.92 - 47.87: 90 47.87 - 63.83: 36 63.83 - 79.79: 5 Dihedral angle restraints: 3192 sinusoidal: 1689 harmonic: 1503 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 167.77 -74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 6.33 72.67 1 2.00e+01 2.50e-03 1.69e+01 dihedral pdb=" CA PHE H 27 " pdb=" C PHE H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 254 0.027 - 0.053: 150 0.053 - 0.080: 50 0.080 - 0.107: 23 0.107 - 0.133: 15 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 100 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO L 101 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 101 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 101 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO L 65 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " -0.019 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 853 2.24 - 2.83: 13946 2.83 - 3.42: 15347 3.42 - 4.01: 21243 4.01 - 4.60: 31822 Nonbonded interactions: 83211 Sorted by model distance: nonbonded pdb=" O SER A 366 " pdb="HD22 ASN A 370 " model vdw 1.650 2.450 nonbonded pdb=" O PHE A 392 " pdb=" H THR A 523 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN A 474 " pdb=" H GLN A 474 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN H 13 " pdb=" H GLN H 13 " model vdw 1.668 2.450 nonbonded pdb=" OD1 ASP H 109 " pdb=" H VAL H 110 " model vdw 1.671 2.450 ... (remaining 83206 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: 0.360 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: 0.040 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.270 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: 9.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 0.046 3426 Z= 0.139 Angle : 0.585 4.978 4662 Z= 0.327 Chirality : 0.043 0.133 492 Planarity : 0.005 0.051 605 Dihedral : 13.977 79.788 1231 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.62 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.38), residues: 420 helix: -3.67 (0.71), residues: 21 sheet: -1.29 (0.47), residues: 122 loop : -2.24 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 67 TYR 0.013 0.001 TYR A 380 PHE 0.014 0.001 PHE L 77 TRP 0.006 0.001 TRP L 41 HIS 0.002 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3419) covalent geometry : angle 0.58412 ( 4647) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.84173 ( 12) hydrogen bonds : bond 0.14705 ( 79) hydrogen bonds : angle 9.17299 ( 207) link_NAG-ASN : bond 0.00333 ( 1) link_NAG-ASN : angle 0.87456 ( 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8760 (m-30) cc_final: 0.8492 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1786 time to fit residues: 17.2177 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 : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.053599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044447 restraints weight = 50230.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047237 restraints weight = 21236.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049133 restraints weight = 11279.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050408 restraints weight = 6730.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051267 restraints weight = 4287.524| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3426 Z= 0.147 Angle : 0.559 4.817 4662 Z= 0.304 Chirality : 0.041 0.137 492 Planarity : 0.005 0.049 605 Dihedral : 5.589 42.942 494 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.39), residues: 420 helix: -2.98 (0.81), residues: 27 sheet: -1.33 (0.47), residues: 123 loop : -2.13 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.019 0.001 TYR A 489 PHE 0.011 0.001 PHE L 77 TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3419) covalent geometry : angle 0.55601 ( 4647) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.11450 ( 12) hydrogen bonds : bond 0.03262 ( 79) hydrogen bonds : angle 6.44153 ( 207) link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 1.22080 ( 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 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.9454 (ttm110) cc_final: 0.8994 (mtp85) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1668 time to fit residues: 14.2297 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.040074 restraints weight = 53587.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042544 restraints weight = 22693.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.044278 restraints weight = 12237.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045477 restraints weight = 7472.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046323 restraints weight = 4848.039| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3426 Z= 0.281 Angle : 0.646 5.396 4662 Z= 0.349 Chirality : 0.040 0.123 492 Planarity : 0.006 0.080 605 Dihedral : 5.695 32.998 494 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.38), residues: 420 helix: -3.51 (0.71), residues: 27 sheet: -1.62 (0.45), residues: 126 loop : -2.02 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 457 TYR 0.016 0.002 TYR A 351 PHE 0.024 0.002 PHE A 486 TRP 0.005 0.001 TRP A 436 HIS 0.005 0.002 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 3419) covalent geometry : angle 0.64390 ( 4647) SS BOND : bond 0.00415 ( 6) SS BOND : angle 0.94491 ( 12) hydrogen bonds : bond 0.03891 ( 79) hydrogen bonds : angle 6.16372 ( 207) link_NAG-ASN : bond 0.00466 ( 1) link_NAG-ASN : angle 1.40695 ( 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 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9032 (t0) cc_final: 0.8805 (t0) REVERT: H 59 TYR cc_start: 0.8793 (m-80) cc_final: 0.8163 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1945 time to fit residues: 14.4792 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040239 restraints weight = 53677.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042694 restraints weight = 23084.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.044319 restraints weight = 12559.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.045577 restraints weight = 7908.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046444 restraints weight = 5130.600| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3426 Z= 0.175 Angle : 0.566 5.317 4662 Z= 0.304 Chirality : 0.040 0.137 492 Planarity : 0.006 0.075 605 Dihedral : 5.477 34.322 494 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.71 (0.39), residues: 420 helix: -3.45 (0.76), residues: 27 sheet: -1.21 (0.47), residues: 118 loop : -1.98 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.011 0.001 TYR A 489 PHE 0.017 0.001 PHE L 77 TRP 0.010 0.001 TRP H 36 HIS 0.005 0.002 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3419) covalent geometry : angle 0.56284 ( 4647) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.09104 ( 12) hydrogen bonds : bond 0.03156 ( 79) hydrogen bonds : angle 5.97941 ( 207) link_NAG-ASN : bond 0.00367 ( 1) link_NAG-ASN : angle 1.33275 ( 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 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8994 (t0) cc_final: 0.8776 (t0) REVERT: A 471 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7859 (mm-30) REVERT: H 22 CYS cc_start: 0.5593 (t) cc_final: 0.5375 (t) REVERT: H 34 MET cc_start: 0.9182 (mtt) cc_final: 0.8867 (mmm) REVERT: H 59 TYR cc_start: 0.8725 (m-80) cc_final: 0.8112 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1785 time to fit residues: 13.4584 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040236 restraints weight = 53547.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042694 restraints weight = 23077.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.044434 restraints weight = 12612.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045623 restraints weight = 7769.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046497 restraints weight = 5098.815| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3426 Z= 0.156 Angle : 0.561 5.140 4662 Z= 0.302 Chirality : 0.040 0.138 492 Planarity : 0.005 0.069 605 Dihedral : 5.359 35.728 494 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.40), residues: 420 helix: -3.31 (0.79), residues: 27 sheet: -1.06 (0.46), residues: 123 loop : -1.97 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.011 0.001 TYR A 489 PHE 0.018 0.001 PHE L 77 TRP 0.005 0.001 TRP H 36 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3419) covalent geometry : angle 0.55874 ( 4647) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.06865 ( 12) hydrogen bonds : bond 0.03102 ( 79) hydrogen bonds : angle 5.86102 ( 207) link_NAG-ASN : bond 0.00352 ( 1) link_NAG-ASN : angle 1.30964 ( 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 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7913 (mm-30) REVERT: H 59 TYR cc_start: 0.8752 (m-80) cc_final: 0.8270 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1559 time to fit residues: 11.8967 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.041468 restraints weight = 51977.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044003 restraints weight = 22313.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.045804 restraints weight = 12153.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047041 restraints weight = 7437.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047924 restraints weight = 4831.331| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3426 Z= 0.097 Angle : 0.529 5.131 4662 Z= 0.282 Chirality : 0.041 0.144 492 Planarity : 0.005 0.066 605 Dihedral : 5.237 39.139 494 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.40), residues: 420 helix: -3.13 (0.80), residues: 27 sheet: -1.09 (0.44), residues: 123 loop : -1.81 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.013 0.001 TYR L 93 PHE 0.012 0.001 PHE L 77 TRP 0.016 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3419) covalent geometry : angle 0.52659 ( 4647) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.89165 ( 12) hydrogen bonds : bond 0.02688 ( 79) hydrogen bonds : angle 5.69590 ( 207) link_NAG-ASN : bond 0.00310 ( 1) link_NAG-ASN : angle 1.33463 ( 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 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8914 (t0) cc_final: 0.8680 (t0) REVERT: A 471 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7909 (mm-30) REVERT: H 59 TYR cc_start: 0.8734 (m-80) cc_final: 0.8295 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1754 time to fit residues: 13.3053 Evaluate side-chains 56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.039616 restraints weight = 54168.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041986 restraints weight = 23774.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043672 restraints weight = 13021.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044803 restraints weight = 7961.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045615 restraints weight = 5158.620| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3426 Z= 0.201 Angle : 0.575 4.544 4662 Z= 0.310 Chirality : 0.040 0.127 492 Planarity : 0.006 0.062 605 Dihedral : 5.458 36.087 494 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.39), residues: 420 helix: -3.44 (0.76), residues: 26 sheet: -1.02 (0.45), residues: 124 loop : -1.92 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.012 0.002 TYR H 80 PHE 0.019 0.002 PHE L 77 TRP 0.011 0.001 TRP A 436 HIS 0.001 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 3419) covalent geometry : angle 0.57332 ( 4647) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.92362 ( 12) hydrogen bonds : bond 0.03317 ( 79) hydrogen bonds : angle 5.72311 ( 207) link_NAG-ASN : bond 0.00436 ( 1) link_NAG-ASN : angle 1.34054 ( 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 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8956 (t0) cc_final: 0.8711 (t0) REVERT: H 34 MET cc_start: 0.9238 (mtt) cc_final: 0.8910 (mmm) REVERT: H 59 TYR cc_start: 0.8854 (m-80) cc_final: 0.8388 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1830 time to fit residues: 12.3745 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.049242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.040663 restraints weight = 52400.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043151 restraints weight = 22411.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.044835 restraints weight = 12150.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.046042 restraints weight = 7545.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.046891 restraints weight = 4863.845| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3426 Z= 0.104 Angle : 0.533 5.029 4662 Z= 0.285 Chirality : 0.041 0.145 492 Planarity : 0.005 0.060 605 Dihedral : 5.264 39.124 494 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.40), residues: 420 helix: -3.29 (0.80), residues: 26 sheet: -1.00 (0.44), residues: 124 loop : -1.72 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.010 0.001 TYR L 93 PHE 0.014 0.001 PHE L 77 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3419) covalent geometry : angle 0.53080 ( 4647) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.80434 ( 12) hydrogen bonds : bond 0.02736 ( 79) hydrogen bonds : angle 5.59208 ( 207) link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 1.37184 ( 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 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8952 (t0) cc_final: 0.8722 (t0) REVERT: H 59 TYR cc_start: 0.8775 (m-80) cc_final: 0.8300 (m-80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1791 time to fit residues: 12.7151 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039775 restraints weight = 53676.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042129 restraints weight = 23264.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043843 restraints weight = 12862.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.044990 restraints weight = 7870.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045842 restraints weight = 5106.720| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3426 Z= 0.132 Angle : 0.545 4.654 4662 Z= 0.291 Chirality : 0.041 0.134 492 Planarity : 0.005 0.060 605 Dihedral : 5.327 38.803 494 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.40), residues: 420 helix: -3.22 (0.81), residues: 26 sheet: -0.88 (0.46), residues: 113 loop : -1.82 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.012 0.001 TYR A 380 PHE 0.014 0.001 PHE L 77 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3419) covalent geometry : angle 0.54335 ( 4647) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.94448 ( 12) hydrogen bonds : bond 0.02861 ( 79) hydrogen bonds : angle 5.46710 ( 207) link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 1.12869 ( 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 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8938 (t0) cc_final: 0.8696 (t0) REVERT: H 59 TYR cc_start: 0.8836 (m-80) cc_final: 0.8272 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1887 time to fit residues: 12.9799 Evaluate side-chains 52 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.040041 restraints weight = 52392.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042417 restraints weight = 22738.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044133 restraints weight = 12510.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045295 restraints weight = 7670.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046088 restraints weight = 4956.809| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3426 Z= 0.114 Angle : 0.537 4.965 4662 Z= 0.284 Chirality : 0.041 0.139 492 Planarity : 0.006 0.072 605 Dihedral : 5.259 39.947 494 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.40), residues: 420 helix: -3.19 (0.82), residues: 26 sheet: -0.87 (0.45), residues: 115 loop : -1.80 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 466 TYR 0.009 0.001 TYR H 94 PHE 0.014 0.001 PHE L 77 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3419) covalent geometry : angle 0.53485 ( 4647) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.97904 ( 12) hydrogen bonds : bond 0.02709 ( 79) hydrogen bonds : angle 5.41354 ( 207) link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 1.18948 ( 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 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8929 (t0) cc_final: 0.8710 (t0) REVERT: A 484 GLU cc_start: 0.8077 (tp30) cc_final: 0.7702 (tp30) REVERT: H 34 MET cc_start: 0.9390 (mtm) cc_final: 0.8863 (mmm) REVERT: H 59 TYR cc_start: 0.8836 (m-80) cc_final: 0.8281 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1668 time to fit residues: 10.9822 Evaluate side-chains 49 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040979 restraints weight = 52698.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043395 restraints weight = 22918.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.045137 restraints weight = 12534.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046265 restraints weight = 7588.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047087 restraints weight = 4917.457| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3426 Z= 0.091 Angle : 0.525 4.675 4662 Z= 0.277 Chirality : 0.042 0.141 492 Planarity : 0.005 0.059 605 Dihedral : 5.214 42.255 494 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.40), residues: 420 helix: -3.20 (0.94), residues: 20 sheet: -0.80 (0.44), residues: 120 loop : -1.74 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.009 0.001 TYR A 489 PHE 0.012 0.001 PHE H 68 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 3419) covalent geometry : angle 0.52353 ( 4647) SS BOND : bond 0.00235 ( 6) SS BOND : angle 0.80358 ( 12) hydrogen bonds : bond 0.02615 ( 79) hydrogen bonds : angle 5.28744 ( 207) link_NAG-ASN : bond 0.00340 ( 1) link_NAG-ASN : angle 1.19569 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.47 seconds wall clock time: 23 minutes 52.11 seconds (1432.11 seconds total)