Starting phenix.real_space_refine on Thu Jul 24 02:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eng_31210/07_2025/7eng_31210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eng_31210/07_2025/7eng_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_31210/07_2025/7eng_31210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2025/7eng_31210.map" model { file = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2025/7eng_31210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2025/7eng_31210.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.51, per 1000 atoms: 0.91 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: 1.31 Conformation dependent library (CDL) restraints added in 810.1 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: 0.73 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: 1.56 Time building geometry restraints manager: 1.59 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: 13.300 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- 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 : 14.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (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 TRP 0.013 0.002 TRP L 56 HIS 0.005 0.001 HIS L 95 PHE 0.018 0.002 PHE L 215 TYR 0.022 0.002 TYR L 31 ARG 0.007 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 1) link_NAG-ASN : angle 6.85152 ( 3) link_BETA1-4 : bond 0.00700 ( 1) link_BETA1-4 : angle 3.25111 ( 3) hydrogen bonds : bond 0.17659 ( 143) hydrogen bonds : angle 8.71255 ( 399) SS BOND : bond 0.00795 ( 6) SS BOND : angle 2.14287 ( 12) covalent geometry : bond 0.00664 ( 5077) covalent geometry : angle 0.82509 ( 6913) *********************** 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 : 0.539 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: 0.2052 time to fit residues: 21.5370 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 : 0.539 ------------------------------------------------------------------------------- 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 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 H 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.210702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.181197 restraints weight = 5926.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.178269 restraints weight = 10588.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180109 restraints weight = 9112.225| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5085 Z= 0.153 Angle : 0.683 8.580 6931 Z= 0.345 Chirality : 0.048 0.342 768 Planarity : 0.005 0.049 890 Dihedral : 12.052 81.665 742 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.54 % Allowed : 9.80 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.32), residues: 634 helix: -3.22 (0.75), residues: 34 sheet: -1.08 (0.32), residues: 252 loop : -1.70 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.002 HIS L 204 PHE 0.015 0.002 PHE L 145 TYR 0.015 0.002 TYR L 31 ARG 0.004 0.001 ARG L 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 1) link_NAG-ASN : angle 4.61015 ( 3) link_BETA1-4 : bond 0.00972 ( 1) link_BETA1-4 : angle 4.46292 ( 3) hydrogen bonds : bond 0.03569 ( 143) hydrogen bonds : angle 7.27712 ( 399) SS BOND : bond 0.00557 ( 6) SS BOND : angle 1.46345 ( 12) covalent geometry : bond 0.00352 ( 5077) covalent geometry : angle 0.66830 ( 6913) *********************** 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 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7257 (p90) cc_final: 0.6973 (p90) REVERT: H 90 ASP cc_start: 0.8486 (m-30) cc_final: 0.8280 (m-30) REVERT: B 383 SER cc_start: 0.8176 (t) cc_final: 0.7965 (p) outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.2683 time to fit residues: 25.1144 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 58 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.210818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.182702 restraints weight = 5985.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180923 restraints weight = 10493.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177670 restraints weight = 8712.542| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5085 Z= 0.161 Angle : 0.652 8.188 6931 Z= 0.327 Chirality : 0.046 0.342 768 Planarity : 0.004 0.035 890 Dihedral : 8.878 56.378 741 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.45 % Allowed : 12.70 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.33), residues: 634 helix: -3.15 (0.75), residues: 35 sheet: -0.79 (0.32), residues: 242 loop : -1.63 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.002 PHE H 156 TYR 0.021 0.002 TYR H 155 ARG 0.004 0.001 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 1) link_NAG-ASN : angle 4.06401 ( 3) link_BETA1-4 : bond 0.01585 ( 1) link_BETA1-4 : angle 3.67457 ( 3) hydrogen bonds : bond 0.03466 ( 143) hydrogen bonds : angle 7.05013 ( 399) SS BOND : bond 0.00782 ( 6) SS BOND : angle 1.54407 ( 12) covalent geometry : bond 0.00377 ( 5077) covalent geometry : angle 0.63998 ( 6913) *********************** 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 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 146 TYR cc_start: 0.8343 (t80) cc_final: 0.8069 (t80) REVERT: H 53 TYR cc_start: 0.7171 (p90) cc_final: 0.6920 (p90) REVERT: B 383 SER cc_start: 0.8275 (t) cc_final: 0.8044 (p) outliers start: 8 outliers final: 5 residues processed: 78 average time/residue: 0.4422 time to fit residues: 46.6457 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 99 ASP 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 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.210263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181379 restraints weight = 5955.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178992 restraints weight = 10990.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180710 restraints weight = 9694.424| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2002 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= 0.157 Angle : 0.638 9.257 6931 Z= 0.318 Chirality : 0.045 0.317 768 Planarity : 0.004 0.033 890 Dihedral : 7.452 49.157 741 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.54 % Allowed : 13.61 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.32), residues: 634 helix: -3.18 (0.66), residues: 41 sheet: -0.66 (0.33), residues: 234 loop : -1.63 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE L 124 TYR 0.019 0.002 TYR H 155 ARG 0.003 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 1) link_NAG-ASN : angle 3.18558 ( 3) link_BETA1-4 : bond 0.01459 ( 1) link_BETA1-4 : angle 4.06050 ( 3) hydrogen bonds : bond 0.03218 ( 143) hydrogen bonds : angle 6.88364 ( 399) SS BOND : bond 0.00799 ( 6) SS BOND : angle 1.44934 ( 12) covalent geometry : bond 0.00368 ( 5077) covalent geometry : angle 0.62682 ( 6913) *********************** 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 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7274 (p90) cc_final: 0.7015 (p90) REVERT: H 90 ASP cc_start: 0.8456 (m-30) cc_final: 0.8125 (m-30) REVERT: H 156 PHE cc_start: 0.7755 (t80) cc_final: 0.7555 (t80) REVERT: B 383 SER cc_start: 0.8259 (t) cc_final: 0.8029 (p) REVERT: B 408 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6151 (ptm160) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.3908 time to fit residues: 43.7839 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 : 1.733 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.212480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162958 restraints weight = 6142.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.164526 restraints weight = 5321.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165440 restraints weight = 4642.734| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5085 Z= 0.189 Angle : 0.661 9.013 6931 Z= 0.329 Chirality : 0.046 0.364 768 Planarity : 0.004 0.035 890 Dihedral : 7.011 49.005 741 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.72 % Allowed : 15.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.33), residues: 634 helix: -3.08 (0.67), residues: 41 sheet: -0.71 (0.33), residues: 236 loop : -1.59 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.008 0.001 HIS H 35 PHE 0.015 0.001 PHE H 68 TYR 0.021 0.002 TYR B 396 ARG 0.005 0.001 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 1) link_NAG-ASN : angle 4.44401 ( 3) link_BETA1-4 : bond 0.01295 ( 1) link_BETA1-4 : angle 4.56980 ( 3) hydrogen bonds : bond 0.03295 ( 143) hydrogen bonds : angle 6.78992 ( 399) SS BOND : bond 0.00863 ( 6) SS BOND : angle 1.71695 ( 12) covalent geometry : bond 0.00447 ( 5077) covalent geometry : angle 0.64425 ( 6913) *********************** 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 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8535 (mmm) cc_final: 0.7915 (mmm) REVERT: H 53 TYR cc_start: 0.7336 (p90) cc_final: 0.7064 (p90) REVERT: H 90 ASP cc_start: 0.8589 (m-30) cc_final: 0.8302 (m-30) REVERT: H 220 LYS cc_start: 0.6664 (ttpt) cc_final: 0.6414 (ttpt) REVERT: B 383 SER cc_start: 0.8397 (t) cc_final: 0.8087 (p) REVERT: B 408 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6642 (ptm160) outliers start: 15 outliers final: 11 residues processed: 73 average time/residue: 0.2977 time to fit residues: 28.3972 Evaluate side-chains 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.211317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177458 restraints weight = 5935.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173627 restraints weight = 9856.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.176116 restraints weight = 10493.078| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2322 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= 0.129 Angle : 0.611 7.722 6931 Z= 0.305 Chirality : 0.045 0.301 768 Planarity : 0.004 0.032 890 Dihedral : 6.536 49.966 741 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.33), residues: 634 helix: -3.00 (0.68), residues: 41 sheet: -0.63 (0.33), residues: 236 loop : -1.55 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 PHE 0.024 0.001 PHE H 156 TYR 0.016 0.001 TYR B 421 ARG 0.003 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 1) link_NAG-ASN : angle 3.43500 ( 3) link_BETA1-4 : bond 0.01171 ( 1) link_BETA1-4 : angle 4.57267 ( 3) hydrogen bonds : bond 0.03052 ( 143) hydrogen bonds : angle 6.70074 ( 399) SS BOND : bond 0.00650 ( 6) SS BOND : angle 1.38176 ( 12) covalent geometry : bond 0.00303 ( 5077) covalent geometry : angle 0.59774 ( 6913) *********************** 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 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: H 90 ASP cc_start: 0.8526 (m-30) cc_final: 0.8253 (m-30) REVERT: H 173 VAL cc_start: 0.8049 (t) cc_final: 0.7831 (m) REVERT: B 383 SER cc_start: 0.8350 (t) cc_final: 0.8075 (p) REVERT: B 408 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6500 (ptm160) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.4911 time to fit residues: 49.8121 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.0970 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.208362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176140 restraints weight = 5894.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.173733 restraints weight = 9077.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.176433 restraints weight = 9009.373| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5085 Z= 0.196 Angle : 0.648 7.372 6931 Z= 0.326 Chirality : 0.046 0.354 768 Planarity : 0.004 0.032 890 Dihedral : 6.526 51.323 741 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.54 % Allowed : 16.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.33), residues: 634 helix: -2.95 (0.69), residues: 41 sheet: -0.63 (0.33), residues: 234 loop : -1.58 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.007 0.001 HIS H 35 PHE 0.020 0.002 PHE H 68 TYR 0.016 0.002 TYR L 55 ARG 0.003 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 1) link_NAG-ASN : angle 4.46478 ( 3) link_BETA1-4 : bond 0.01018 ( 1) link_BETA1-4 : angle 4.55055 ( 3) hydrogen bonds : bond 0.03265 ( 143) hydrogen bonds : angle 6.67980 ( 399) SS BOND : bond 0.00847 ( 6) SS BOND : angle 1.77964 ( 12) covalent geometry : bond 0.00466 ( 5077) covalent geometry : angle 0.63035 ( 6913) *********************** 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 73 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8386 (mmm) cc_final: 0.7668 (mmm) REVERT: L 27 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: H 90 ASP cc_start: 0.8525 (m-30) cc_final: 0.8179 (m-30) REVERT: H 156 PHE cc_start: 0.7567 (t80) cc_final: 0.7361 (t80) REVERT: H 220 LYS cc_start: 0.6949 (ttpt) cc_final: 0.6730 (ttpt) REVERT: B 383 SER cc_start: 0.8338 (t) cc_final: 0.8036 (p) REVERT: B 408 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6508 (ptm160) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1687 time to fit residues: 15.5630 Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.213529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167948 restraints weight = 6123.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167566 restraints weight = 4778.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.167787 restraints weight = 4269.506| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5085 Z= 0.149 Angle : 0.616 8.060 6931 Z= 0.310 Chirality : 0.045 0.322 768 Planarity : 0.004 0.031 890 Dihedral : 6.340 52.427 741 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.36 % Allowed : 17.60 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.33), residues: 634 helix: -2.87 (0.70), residues: 41 sheet: -0.59 (0.33), residues: 234 loop : -1.53 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.007 0.002 HIS H 35 PHE 0.024 0.001 PHE H 68 TYR 0.015 0.001 TYR B 396 ARG 0.003 0.000 ARG L 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 1) link_NAG-ASN : angle 3.71897 ( 3) link_BETA1-4 : bond 0.00975 ( 1) link_BETA1-4 : angle 4.52699 ( 3) hydrogen bonds : bond 0.03095 ( 143) hydrogen bonds : angle 6.64024 ( 399) SS BOND : bond 0.00728 ( 6) SS BOND : angle 1.35487 ( 12) covalent geometry : bond 0.00351 ( 5077) covalent geometry : angle 0.60247 ( 6913) *********************** 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 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: H 90 ASP cc_start: 0.8544 (m-30) cc_final: 0.8239 (m-30) REVERT: H 220 LYS cc_start: 0.6739 (ttpt) cc_final: 0.6500 (ttpt) REVERT: B 383 SER cc_start: 0.8335 (t) cc_final: 0.8028 (p) REVERT: B 408 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6584 (ptm160) outliers start: 13 outliers final: 11 residues processed: 64 average time/residue: 0.2914 time to fit residues: 24.4547 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 : 1.044 ------------------------------------------------------------------------------- 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 5 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 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 = 0.4477 r_free = 0.4477 target = 0.214313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183237 restraints weight = 6006.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.183237 restraints weight = 12838.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.184893 restraints weight = 9474.169| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2577 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= 0.143 Angle : 0.610 7.435 6931 Z= 0.308 Chirality : 0.045 0.313 768 Planarity : 0.004 0.031 890 Dihedral : 6.228 56.093 741 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.54 % Allowed : 17.42 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.33), residues: 634 helix: -2.82 (0.70), residues: 41 sheet: -0.54 (0.33), residues: 234 loop : -1.52 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.028 0.001 PHE H 156 TYR 0.016 0.001 TYR H 155 ARG 0.003 0.000 ARG L 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 1) link_NAG-ASN : angle 3.60507 ( 3) link_BETA1-4 : bond 0.00946 ( 1) link_BETA1-4 : angle 4.46962 ( 3) hydrogen bonds : bond 0.03059 ( 143) hydrogen bonds : angle 6.57439 ( 399) SS BOND : bond 0.00679 ( 6) SS BOND : angle 1.40051 ( 12) covalent geometry : bond 0.00336 ( 5077) covalent geometry : angle 0.59589 ( 6913) *********************** 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 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: H 90 ASP cc_start: 0.8547 (m-30) cc_final: 0.8238 (m-30) REVERT: H 220 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6778 (ttpt) REVERT: B 383 SER cc_start: 0.8336 (t) cc_final: 0.8068 (p) REVERT: B 408 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6496 (ptm160) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.2403 time to fit residues: 20.9697 Evaluate side-chains 69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 5 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 11 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.213118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.183588 restraints weight = 6068.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182040 restraints weight = 12402.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182304 restraints weight = 9282.503| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5085 Z= 0.173 Angle : 0.621 7.344 6931 Z= 0.314 Chirality : 0.045 0.329 768 Planarity : 0.004 0.031 890 Dihedral : 6.357 58.922 741 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.72 % Allowed : 17.60 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.33), residues: 634 helix: -2.79 (0.70), residues: 41 sheet: -0.54 (0.33), residues: 234 loop : -1.56 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 PHE 0.026 0.002 PHE H 156 TYR 0.018 0.002 TYR B 396 ARG 0.004 0.001 ARG L 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 3.90731 ( 3) link_BETA1-4 : bond 0.00893 ( 1) link_BETA1-4 : angle 4.39371 ( 3) hydrogen bonds : bond 0.03154 ( 143) hydrogen bonds : angle 6.60382 ( 399) SS BOND : bond 0.00743 ( 6) SS BOND : angle 1.41676 ( 12) covalent geometry : bond 0.00410 ( 5077) covalent geometry : angle 0.60689 ( 6913) ********************** 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 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8309 (mmm) cc_final: 0.7692 (mmm) REVERT: L 27 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: H 90 ASP cc_start: 0.8559 (m-30) cc_final: 0.8249 (m-30) REVERT: H 220 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6784 (ttpt) REVERT: B 383 SER cc_start: 0.8328 (t) cc_final: 0.8006 (p) REVERT: B 408 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6507 (ptm160) REVERT: B 428 ASP cc_start: 0.7606 (p0) cc_final: 0.7354 (p0) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.2392 time to fit residues: 21.9988 Evaluate side-chains 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 5 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 H residue 193 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 59 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.211111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181986 restraints weight = 5964.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179017 restraints weight = 11125.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178571 restraints weight = 9179.371| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2650 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 : 0.605 7.301 6931 Z= 0.307 Chirality : 0.045 0.313 768 Planarity : 0.004 0.031 890 Dihedral : 6.217 59.168 741 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.27 % Allowed : 17.24 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.33), residues: 634 helix: -2.75 (0.70), residues: 41 sheet: -0.51 (0.33), residues: 234 loop : -1.54 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 PHE 0.019 0.001 PHE H 68 TYR 0.017 0.001 TYR B 396 ARG 0.005 0.000 ARG L 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 1) link_NAG-ASN : angle 3.61044 ( 3) link_BETA1-4 : bond 0.00924 ( 1) link_BETA1-4 : angle 4.34340 ( 3) hydrogen bonds : bond 0.03051 ( 143) hydrogen bonds : angle 6.55463 ( 399) SS BOND : bond 0.00675 ( 6) SS BOND : angle 1.35058 ( 12) covalent geometry : bond 0.00348 ( 5077) covalent geometry : angle 0.59199 ( 6913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.10 seconds wall clock time: 59 minutes 26.23 seconds (3566.23 seconds total)