Starting phenix.real_space_refine on Tue Mar 3 13:17:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eng_31210/03_2026/7eng_31210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eng_31210/03_2026/7eng_31210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_2026/7eng_31210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_2026/7eng_31210.map" model { file = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_2026/7eng_31210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_2026/7eng_31210.cif" } resolution = 3.59 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= 1.000 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 22 5.16 5 C 3127 2.51 5 N 826 2.21 5 O 979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s 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: 4954 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.07, per 1000 atoms: 0.22 Number of scatterers: 4954 At special positions: 0 Unit cell: (93.7251, 87.2613, 108.807, 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 22 16.00 O 979 8.00 N 826 7.00 C 3127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 285.9 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 11.7% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.519A pdb=" N ASP L 88 " --> pdb=" O GLN L 85 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 85 through 89' Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.553A pdb=" N TYR L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS L 194 " --> pdb=" O ALA L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.200A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.084A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.772A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.575A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.611A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'L' and resid 151 through 156 removed outlier: 3.875A pdb=" N LYS L 151 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 202 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 211 " --> pdb=" O VAL L 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 60 removed outlier: 4.028A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 112 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.323A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.323A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.051A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.612A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 158 hydrogen bonds defined for protein. 399 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: 0.57 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 805 1.31 - 1.44: 1466 1.44 - 1.57: 2781 1.57 - 1.70: 0 1.70 - 1.83: 25 Bond restraints: 5077 Sorted by residual: bond pdb=" C7 NAG A 1 " pdb=" N2 NAG A 1 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C7 NAG A 2 " pdb=" N2 NAG A 2 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.38e+00 ... (remaining 5072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 6673 2.02 - 4.03: 199 4.03 - 6.05: 35 6.05 - 8.07: 4 8.07 - 10.08: 2 Bond angle restraints: 6913 Sorted by residual: angle pdb=" C SER H 140 " pdb=" N THR H 141 " pdb=" CA THR H 141 " ideal model delta sigma weight residual 122.42 112.34 10.08 1.33e+00 5.65e-01 5.75e+01 angle pdb=" N PRO H 133 " pdb=" CA PRO H 133 " pdb=" C PRO H 133 " ideal model delta sigma weight residual 111.38 117.90 -6.52 1.59e+00 3.96e-01 1.68e+01 angle pdb=" N SER H 137 " pdb=" CA SER H 137 " pdb=" C SER H 137 " ideal model delta sigma weight residual 111.28 107.11 4.17 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CB GLN L 6 " pdb=" CG GLN L 6 " pdb=" CD GLN L 6 " ideal model delta sigma weight residual 112.60 106.33 6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" N LYS H 139 " pdb=" CA LYS H 139 " pdb=" C LYS H 139 " ideal model delta sigma weight residual 113.97 109.49 4.48 1.28e+00 6.10e-01 1.22e+01 ... (remaining 6908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.72: 2840 23.72 - 47.44: 152 47.44 - 71.16: 25 71.16 - 94.88: 14 94.88 - 118.60: 8 Dihedral angle restraints: 3039 sinusoidal: 1177 harmonic: 1862 Sorted by residual: dihedral pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" N PHE B 338 " pdb=" CA PHE B 338 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS L 140 " pdb=" SG CYS L 140 " pdb=" SG CYS L 200 " pdb=" CB CYS L 200 " ideal model delta sinusoidal sigma weight residual 93.00 51.38 41.62 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CA SER L 33 " pdb=" C SER L 33 " pdb=" N ASN L 34 " pdb=" CA ASN L 34 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 710 0.092 - 0.183: 54 0.183 - 0.274: 2 0.274 - 0.366: 1 0.366 - 0.457: 1 Chirality restraints: 768 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU H 134 " pdb=" N LEU H 134 " pdb=" C LEU H 134 " pdb=" CB LEU H 134 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB THR H 100 " pdb=" CA THR H 100 " pdb=" OG1 THR H 100 " pdb=" CG2 THR H 100 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 765 not shown) Planarity restraints: 891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 132 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" C PHE H 132 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE H 132 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO H 133 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO L 49 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO L 50 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET L 4 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C MET L 4 " 0.026 2.00e-02 2.50e+03 pdb=" O MET L 4 " -0.010 2.00e-02 2.50e+03 pdb=" N THR L 5 " -0.009 2.00e-02 2.50e+03 ... (remaining 888 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 515 2.74 - 3.28: 4860 3.28 - 3.82: 7939 3.82 - 4.36: 9396 4.36 - 4.90: 16619 Nonbonded interactions: 39329 Sorted by model distance: nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.204 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.249 3.040 nonbonded pdb=" NE2 GLN B 474 " pdb=" O THR B 478 " model vdw 2.254 3.120 nonbonded pdb=" OG SER L 33 " pdb=" N SER B 349 " model vdw 2.255 3.120 ... (remaining 39324 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: 4.730 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: 0.020 Set scattering table: 0.010 Process input model: 6.200 Find NCS groups from input model: 0.030 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 5085 Z= 0.322 Angle : 0.844 10.940 6931 Z= 0.461 Chirality : 0.053 0.457 768 Planarity : 0.005 0.051 890 Dihedral : 17.374 118.598 1835 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.36 % Allowed : 0.91 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 (0.32), residues: 634 helix: -3.42 (0.70), residues: 41 sheet: -1.32 (0.31), residues: 254 loop : -1.92 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.022 0.002 TYR L 31 PHE 0.018 0.002 PHE L 215 TRP 0.013 0.002 TRP L 56 HIS 0.005 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 5077) covalent geometry : angle 0.82509 ( 6913) SS BOND : bond 0.00795 ( 6) SS BOND : angle 2.14287 ( 12) hydrogen bonds : bond 0.17659 ( 143) hydrogen bonds : angle 8.71255 ( 399) link_BETA1-4 : bond 0.00700 ( 1) link_BETA1-4 : angle 3.25111 ( 3) link_NAG-ASN : bond 0.00409 ( 1) link_NAG-ASN : angle 6.85152 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 30 LEU cc_start: 0.8286 (tt) cc_final: 0.8060 (tp) REVERT: H 53 TYR cc_start: 0.7338 (p90) cc_final: 0.7068 (p90) REVERT: H 60 TYR cc_start: 0.8269 (m-80) cc_final: 0.7968 (m-80) REVERT: H 161 THR cc_start: 0.7024 (p) cc_final: 0.6816 (p) REVERT: B 467 ASP cc_start: 0.7461 (p0) cc_final: 0.6930 (p0) outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.0889 time to fit residues: 9.3368 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 130 GLN L 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.211615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.183732 restraints weight = 6036.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179830 restraints weight = 9841.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.179200 restraints weight = 8897.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.177868 restraints weight = 7482.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178849 restraints weight = 6111.816| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5085 Z= 0.140 Angle : 0.676 8.349 6931 Z= 0.341 Chirality : 0.048 0.337 768 Planarity : 0.005 0.053 890 Dihedral : 12.001 80.908 742 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.54 % Allowed : 9.26 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.29 (0.32), residues: 634 helix: -3.21 (0.75), residues: 34 sheet: -1.05 (0.32), residues: 252 loop : -1.68 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 355 TYR 0.013 0.002 TYR L 31 PHE 0.016 0.001 PHE L 145 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS L 204 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5077) covalent geometry : angle 0.66130 ( 6913) SS BOND : bond 0.00552 ( 6) SS BOND : angle 1.38344 ( 12) hydrogen bonds : bond 0.03511 ( 143) hydrogen bonds : angle 7.23162 ( 399) link_BETA1-4 : bond 0.00966 ( 1) link_BETA1-4 : angle 4.45242 ( 3) link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 4.47441 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7260 (p90) cc_final: 0.7031 (p90) REVERT: B 383 SER cc_start: 0.8204 (t) cc_final: 0.7988 (p) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.0957 time to fit residues: 9.3571 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.211417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.175279 restraints weight = 5981.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169281 restraints weight = 6774.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170861 restraints weight = 7882.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171960 restraints weight = 5461.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172658 restraints weight = 4391.007| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5085 Z= 0.148 Angle : 0.644 8.267 6931 Z= 0.323 Chirality : 0.046 0.332 768 Planarity : 0.004 0.033 890 Dihedral : 8.870 56.427 741 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.27 % Allowed : 12.52 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.05 (0.33), residues: 634 helix: -3.08 (0.76), residues: 35 sheet: -0.74 (0.33), residues: 242 loop : -1.62 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.021 0.002 TYR H 155 PHE 0.022 0.001 PHE H 156 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5077) covalent geometry : angle 0.63267 ( 6913) SS BOND : bond 0.00723 ( 6) SS BOND : angle 1.50836 ( 12) hydrogen bonds : bond 0.03409 ( 143) hydrogen bonds : angle 7.02480 ( 399) link_BETA1-4 : bond 0.01990 ( 1) link_BETA1-4 : angle 3.52849 ( 3) link_NAG-ASN : bond 0.00442 ( 1) link_NAG-ASN : angle 3.89588 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 146 TYR cc_start: 0.8327 (t80) cc_final: 0.8018 (t80) REVERT: H 53 TYR cc_start: 0.7262 (p90) cc_final: 0.7010 (p90) REVERT: H 90 ASP cc_start: 0.8493 (m-30) cc_final: 0.8168 (m-30) REVERT: B 383 SER cc_start: 0.8289 (t) cc_final: 0.8037 (p) outliers start: 7 outliers final: 4 residues processed: 81 average time/residue: 0.0933 time to fit residues: 9.4200 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.180245 restraints weight = 5892.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.175852 restraints weight = 9331.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177412 restraints weight = 8673.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.177622 restraints weight = 5999.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.177989 restraints weight = 5121.543| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5085 Z= 0.117 Angle : 0.612 10.044 6931 Z= 0.303 Chirality : 0.044 0.275 768 Planarity : 0.004 0.030 890 Dihedral : 7.200 51.034 741 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.36 % Allowed : 13.25 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.00 (0.32), residues: 634 helix: -3.12 (0.66), residues: 41 sheet: -0.64 (0.33), residues: 239 loop : -1.59 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.020 0.001 TYR H 155 PHE 0.011 0.001 PHE L 124 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5077) covalent geometry : angle 0.60273 ( 6913) SS BOND : bond 0.00959 ( 6) SS BOND : angle 0.97931 ( 12) hydrogen bonds : bond 0.03015 ( 143) hydrogen bonds : angle 6.77941 ( 399) link_BETA1-4 : bond 0.01518 ( 1) link_BETA1-4 : angle 4.03868 ( 3) link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 2.58511 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 146 TYR cc_start: 0.8339 (t80) cc_final: 0.8051 (t80) REVERT: H 53 TYR cc_start: 0.7206 (p90) cc_final: 0.6941 (p90) REVERT: H 90 ASP cc_start: 0.8444 (m-30) cc_final: 0.8194 (m-30) REVERT: B 383 SER cc_start: 0.8318 (t) cc_final: 0.8066 (p) REVERT: B 408 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6424 (ptm160) REVERT: B 420 ASP cc_start: 0.7461 (p0) cc_final: 0.7197 (p0) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.0764 time to fit residues: 7.7833 Evaluate side-chains 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.215002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177651 restraints weight = 6151.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169752 restraints weight = 8034.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.172325 restraints weight = 9251.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173711 restraints weight = 5948.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175204 restraints weight = 4586.849| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5085 Z= 0.147 Angle : 0.622 9.355 6931 Z= 0.308 Chirality : 0.044 0.308 768 Planarity : 0.004 0.029 890 Dihedral : 6.694 53.208 741 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.36 % Allowed : 14.70 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.86 (0.33), residues: 634 helix: -3.00 (0.67), residues: 41 sheet: -0.51 (0.34), residues: 232 loop : -1.52 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 217 TYR 0.018 0.001 TYR H 155 PHE 0.021 0.002 PHE H 68 TRP 0.007 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5077) covalent geometry : angle 0.60990 ( 6913) SS BOND : bond 0.00763 ( 6) SS BOND : angle 1.41030 ( 12) hydrogen bonds : bond 0.03088 ( 143) hydrogen bonds : angle 6.68492 ( 399) link_BETA1-4 : bond 0.01289 ( 1) link_BETA1-4 : angle 4.43475 ( 3) link_NAG-ASN : bond 0.00312 ( 1) link_NAG-ASN : angle 2.93516 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8394 (mmm) cc_final: 0.7717 (mmm) REVERT: H 53 TYR cc_start: 0.7250 (p90) cc_final: 0.7002 (p90) REVERT: H 90 ASP cc_start: 0.8489 (m-30) cc_final: 0.8181 (m-30) REVERT: H 173 VAL cc_start: 0.8016 (t) cc_final: 0.7740 (m) REVERT: H 220 LYS cc_start: 0.6872 (ttpt) cc_final: 0.6609 (ttpt) REVERT: B 383 SER cc_start: 0.8249 (t) cc_final: 0.7992 (p) REVERT: B 408 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6468 (ptm160) REVERT: B 420 ASP cc_start: 0.7537 (p0) cc_final: 0.7307 (p0) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.0770 time to fit residues: 7.3765 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.0470 chunk 4 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.217609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.182590 restraints weight = 6203.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178293 restraints weight = 9695.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181067 restraints weight = 8887.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181954 restraints weight = 5870.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181696 restraints weight = 5644.123| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5085 Z= 0.109 Angle : 0.591 7.643 6931 Z= 0.294 Chirality : 0.044 0.291 768 Planarity : 0.004 0.032 890 Dihedral : 6.302 56.370 741 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.18 % Allowed : 15.43 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.79 (0.33), residues: 634 helix: -2.85 (0.68), residues: 41 sheet: -0.45 (0.33), residues: 234 loop : -1.50 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 217 TYR 0.015 0.001 TYR H 155 PHE 0.018 0.001 PHE H 68 TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5077) covalent geometry : angle 0.57779 ( 6913) SS BOND : bond 0.00609 ( 6) SS BOND : angle 1.16667 ( 12) hydrogen bonds : bond 0.02904 ( 143) hydrogen bonds : angle 6.51553 ( 399) link_BETA1-4 : bond 0.01032 ( 1) link_BETA1-4 : angle 4.74790 ( 3) link_NAG-ASN : bond 0.01032 ( 1) link_NAG-ASN : angle 3.19696 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7203 (p90) cc_final: 0.6963 (p90) REVERT: H 90 ASP cc_start: 0.8393 (m-30) cc_final: 0.8137 (m-30) REVERT: H 173 VAL cc_start: 0.7992 (t) cc_final: 0.7748 (m) REVERT: B 383 SER cc_start: 0.8276 (t) cc_final: 0.8031 (p) REVERT: B 408 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6489 (ptm160) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.0785 time to fit residues: 7.3686 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.214523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187629 restraints weight = 6094.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.187514 restraints weight = 10139.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.187546 restraints weight = 7368.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.186725 restraints weight = 5320.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186861 restraints weight = 5285.296| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5085 Z= 0.169 Angle : 0.619 8.245 6931 Z= 0.309 Chirality : 0.045 0.335 768 Planarity : 0.004 0.030 890 Dihedral : 6.292 55.477 741 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.54 % Allowed : 15.43 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.76 (0.33), residues: 634 helix: -2.83 (0.68), residues: 41 sheet: -0.42 (0.34), residues: 232 loop : -1.49 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 60 TYR 0.014 0.002 TYR L 55 PHE 0.020 0.001 PHE H 68 TRP 0.008 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5077) covalent geometry : angle 0.59909 ( 6913) SS BOND : bond 0.00757 ( 6) SS BOND : angle 1.59158 ( 12) hydrogen bonds : bond 0.03101 ( 143) hydrogen bonds : angle 6.48224 ( 399) link_BETA1-4 : bond 0.00843 ( 1) link_BETA1-4 : angle 4.90019 ( 3) link_NAG-ASN : bond 0.00512 ( 1) link_NAG-ASN : angle 4.87007 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8373 (mmm) cc_final: 0.7665 (mmm) REVERT: L 27 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: H 53 TYR cc_start: 0.7298 (p90) cc_final: 0.7047 (p90) REVERT: H 90 ASP cc_start: 0.8391 (m-30) cc_final: 0.8182 (m-30) REVERT: H 220 LYS cc_start: 0.6954 (ttpt) cc_final: 0.6725 (ttpt) REVERT: B 408 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6551 (ptm160) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.0687 time to fit residues: 6.1542 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.215806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.186962 restraints weight = 6166.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.186404 restraints weight = 10793.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.187895 restraints weight = 8787.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.185949 restraints weight = 6343.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.186426 restraints weight = 5313.649| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5085 Z= 0.142 Angle : 0.604 7.916 6931 Z= 0.302 Chirality : 0.045 0.317 768 Planarity : 0.004 0.029 890 Dihedral : 6.199 57.789 741 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.54 % Allowed : 15.97 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.71 (0.33), residues: 634 helix: -2.64 (0.73), residues: 41 sheet: -0.38 (0.33), residues: 234 loop : -1.48 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.016 0.001 TYR B 396 PHE 0.025 0.002 PHE H 156 TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5077) covalent geometry : angle 0.58581 ( 6913) SS BOND : bond 0.00683 ( 6) SS BOND : angle 1.24868 ( 12) hydrogen bonds : bond 0.02991 ( 143) hydrogen bonds : angle 6.49449 ( 399) link_BETA1-4 : bond 0.00845 ( 1) link_BETA1-4 : angle 4.80371 ( 3) link_NAG-ASN : bond 0.00570 ( 1) link_NAG-ASN : angle 4.63488 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: H 53 TYR cc_start: 0.7279 (p90) cc_final: 0.7051 (p90) REVERT: H 90 ASP cc_start: 0.8455 (m-30) cc_final: 0.8173 (m-30) REVERT: H 220 LYS cc_start: 0.6940 (ttpt) cc_final: 0.6696 (ttpt) REVERT: B 408 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6574 (ptm160) outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.0642 time to fit residues: 5.3340 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.213128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.166717 restraints weight = 6135.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166720 restraints weight = 4907.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166988 restraints weight = 4493.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167082 restraints weight = 4074.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167082 restraints weight = 3870.056| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5085 Z= 0.184 Angle : 0.629 8.931 6931 Z= 0.318 Chirality : 0.046 0.341 768 Planarity : 0.004 0.030 890 Dihedral : 6.333 59.809 741 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.36 % Allowed : 16.52 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.77 (0.33), residues: 634 helix: -2.75 (0.70), residues: 41 sheet: -0.45 (0.34), residues: 234 loop : -1.49 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 60 TYR 0.015 0.002 TYR L 55 PHE 0.023 0.001 PHE H 68 TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 5077) covalent geometry : angle 0.60944 ( 6913) SS BOND : bond 0.00814 ( 6) SS BOND : angle 1.56943 ( 12) hydrogen bonds : bond 0.03171 ( 143) hydrogen bonds : angle 6.55803 ( 399) link_BETA1-4 : bond 0.00832 ( 1) link_BETA1-4 : angle 4.67708 ( 3) link_NAG-ASN : bond 0.00338 ( 1) link_NAG-ASN : angle 5.26558 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8504 (mmm) cc_final: 0.7810 (mmm) REVERT: L 27 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: H 53 TYR cc_start: 0.7308 (p90) cc_final: 0.7080 (p90) REVERT: H 90 ASP cc_start: 0.8535 (m-30) cc_final: 0.8217 (m-30) REVERT: B 383 SER cc_start: 0.8412 (t) cc_final: 0.8069 (p) REVERT: B 408 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6699 (ptm160) outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.0766 time to fit residues: 6.6200 Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.216014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.187999 restraints weight = 6125.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187905 restraints weight = 11146.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.187339 restraints weight = 9260.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.186155 restraints weight = 7651.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.187956 restraints weight = 5855.513| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5085 Z= 0.130 Angle : 0.596 7.716 6931 Z= 0.301 Chirality : 0.045 0.302 768 Planarity : 0.004 0.029 890 Dihedral : 5.987 55.649 741 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.18 % Allowed : 16.70 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.73 (0.33), residues: 634 helix: -2.62 (0.73), residues: 41 sheet: -0.40 (0.34), residues: 234 loop : -1.49 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 217 TYR 0.015 0.001 TYR B 396 PHE 0.016 0.001 PHE H 68 TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5077) covalent geometry : angle 0.58009 ( 6913) SS BOND : bond 0.00657 ( 6) SS BOND : angle 1.26333 ( 12) hydrogen bonds : bond 0.02961 ( 143) hydrogen bonds : angle 6.46952 ( 399) link_BETA1-4 : bond 0.00882 ( 1) link_BETA1-4 : angle 4.60755 ( 3) link_NAG-ASN : bond 0.00504 ( 1) link_NAG-ASN : angle 4.31397 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: H 53 TYR cc_start: 0.7223 (p90) cc_final: 0.7006 (p90) REVERT: H 90 ASP cc_start: 0.8506 (m-30) cc_final: 0.8230 (m-30) REVERT: B 408 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6549 (ptm160) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.0806 time to fit residues: 6.7318 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.0040 chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.218668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.187434 restraints weight = 6230.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.185224 restraints weight = 9703.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186851 restraints weight = 9632.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185032 restraints weight = 6499.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186638 restraints weight = 5512.751| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5085 Z= 0.110 Angle : 0.576 7.565 6931 Z= 0.290 Chirality : 0.044 0.259 768 Planarity : 0.004 0.033 890 Dihedral : 5.576 48.080 741 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.36 % Allowed : 17.06 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.72 (0.33), residues: 634 helix: -2.59 (0.73), residues: 41 sheet: -0.40 (0.34), residues: 236 loop : -1.49 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 355 TYR 0.019 0.001 TYR B 396 PHE 0.027 0.001 PHE H 156 TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5077) covalent geometry : angle 0.56196 ( 6913) SS BOND : bond 0.00576 ( 6) SS BOND : angle 1.08659 ( 12) hydrogen bonds : bond 0.02924 ( 143) hydrogen bonds : angle 6.33027 ( 399) link_BETA1-4 : bond 0.00867 ( 1) link_BETA1-4 : angle 4.49321 ( 3) link_NAG-ASN : bond 0.00447 ( 1) link_NAG-ASN : angle 3.69770 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 987.30 seconds wall clock time: 17 minutes 47.31 seconds (1067.31 seconds total)