Starting phenix.real_space_refine on Thu Mar 6 05:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eng_31210/03_2025/7eng_31210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eng_31210/03_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_31210/03_2025/7eng_31210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_2025/7eng_31210.map" model { file = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_2025/7eng_31210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eng_31210/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.07, per 1000 atoms: 0.82 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: 1.35 Conformation dependent library (CDL) restraints added in 662.7 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: 0.65 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: 1.36 Time building geometry restraints manager: 1.52 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- 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 5077 Z= 0.437 Angle : 0.825 10.081 6913 Z= 0.457 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 *********************** 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 : 0.633 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: 0.2143 time to fit residues: 22.4298 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 : 0.517 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8980 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: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.214722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.184834 restraints weight = 6082.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.183351 restraints weight = 11132.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.183478 restraints weight = 8885.484| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5077 Z= 0.223 Angle : 0.662 8.483 6913 Z= 0.338 Chirality : 0.048 0.349 768 Planarity : 0.005 0.052 890 Dihedral : 11.985 81.623 742 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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 (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 (0.74), 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 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE L 215 TYR 0.013 0.002 TYR L 55 ARG 0.004 0.001 ARG L 217 *********************** 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 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7284 (p90) cc_final: 0.7048 (p90) REVERT: H 60 TYR cc_start: 0.8173 (m-80) cc_final: 0.7965 (m-80) REVERT: H 90 ASP cc_start: 0.8482 (m-30) cc_final: 0.8279 (m-30) REVERT: B 383 SER cc_start: 0.8181 (t) cc_final: 0.7960 (p) outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.2675 time to fit residues: 25.3111 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 : 0.859 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.206268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175419 restraints weight = 5960.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.172719 restraints weight = 10540.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174974 restraints weight = 9399.185| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 5077 Z= 0.386 Angle : 0.699 8.289 6913 Z= 0.357 Chirality : 0.049 0.402 768 Planarity : 0.005 0.044 890 Dihedral : 9.474 60.306 741 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % 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: -2.20 (0.32), residues: 634 helix: -3.15 (0.77), residues: 34 sheet: -0.90 (0.33), residues: 240 loop : -1.69 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.002 PHE H 156 TYR 0.022 0.002 TYR H 155 ARG 0.004 0.001 ARG L 60 *********************** 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 75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7405 (p90) cc_final: 0.7126 (p90) REVERT: H 60 TYR cc_start: 0.8235 (m-80) cc_final: 0.7937 (m-80) REVERT: H 90 ASP cc_start: 0.8501 (m-30) cc_final: 0.8261 (m-30) REVERT: B 383 SER cc_start: 0.8274 (t) cc_final: 0.8039 (p) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.1938 time to fit residues: 18.8013 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 H residue 102 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.211312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175885 restraints weight = 5937.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170201 restraints weight = 8276.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.173037 restraints weight = 7684.280| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5077 Z= 0.207 Angle : 0.622 7.502 6913 Z= 0.313 Chirality : 0.045 0.314 768 Planarity : 0.004 0.035 890 Dihedral : 7.512 47.481 741 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.36 % Allowed : 13.07 % Favored : 84.57 % 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: -2.11 (0.32), residues: 634 helix: -3.22 (0.65), residues: 41 sheet: -0.78 (0.33), residues: 241 loop : -1.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE L 124 TYR 0.020 0.001 TYR H 155 ARG 0.003 0.000 ARG L 60 *********************** 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: 13 poor density : 71 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7264 (p90) cc_final: 0.7026 (p90) REVERT: H 60 TYR cc_start: 0.8178 (m-80) cc_final: 0.7959 (m-80) REVERT: H 90 ASP cc_start: 0.8554 (m-30) cc_final: 0.8307 (m-30) REVERT: B 383 SER cc_start: 0.8251 (t) cc_final: 0.8005 (p) REVERT: B 408 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6299 (ptm160) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 0.2405 time to fit residues: 24.6559 Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4462 r_free = 0.4462 target = 0.212822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184078 restraints weight = 6118.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.183581 restraints weight = 10510.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182036 restraints weight = 8990.914| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5077 Z= 0.268 Angle : 0.640 8.573 6913 Z= 0.324 Chirality : 0.045 0.322 768 Planarity : 0.004 0.035 890 Dihedral : 7.015 47.827 741 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.54 % Allowed : 15.61 % Favored : 81.85 % 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: -2.04 (0.33), residues: 634 helix: -3.09 (0.66), residues: 41 sheet: -0.76 (0.33), residues: 241 loop : -1.56 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.008 0.001 HIS H 35 PHE 0.023 0.002 PHE H 156 TYR 0.021 0.002 TYR B 396 ARG 0.005 0.000 ARG L 60 *********************** 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 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8378 (mmm) cc_final: 0.7650 (mmm) REVERT: H 53 TYR cc_start: 0.7356 (p90) cc_final: 0.7097 (p90) REVERT: H 60 TYR cc_start: 0.8209 (m-80) cc_final: 0.7989 (m-80) REVERT: H 90 ASP cc_start: 0.8495 (m-30) cc_final: 0.8277 (m-30) REVERT: B 383 SER cc_start: 0.8295 (t) cc_final: 0.8022 (p) REVERT: B 408 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6610 (ptm160) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.1867 time to fit residues: 18.1004 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 : 0.549 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.210023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183724 restraints weight = 5915.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.183090 restraints weight = 10171.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.182798 restraints weight = 7632.871| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5077 Z= 0.225 Angle : 0.610 7.982 6913 Z= 0.308 Chirality : 0.045 0.320 768 Planarity : 0.004 0.033 890 Dihedral : 6.628 48.746 741 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.54 % Allowed : 16.52 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.98 (0.33), residues: 634 helix: -2.95 (0.69), residues: 41 sheet: -0.72 (0.33), residues: 241 loop : -1.52 (0.33), residues: 352 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 0.015 0.001 PHE L 124 TYR 0.016 0.001 TYR B 421 ARG 0.004 0.000 ARG L 60 *********************** 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 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8462 (mp10) REVERT: H 53 TYR cc_start: 0.7324 (p90) cc_final: 0.7089 (p90) REVERT: B 383 SER cc_start: 0.8279 (t) cc_final: 0.8013 (p) REVERT: B 408 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6516 (ptm160) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.2231 time to fit residues: 21.0338 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 : 0.541 ------------------------------------------------------------------------------- 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: 0.0040 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 61 optimal weight: 0.0670 chunk 34 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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 = 0.4501 r_free = 0.4501 target = 0.216975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.183576 restraints weight = 6046.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179331 restraints weight = 10229.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.182030 restraints weight = 9547.619| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5077 Z= 0.161 Angle : 0.587 7.242 6913 Z= 0.296 Chirality : 0.044 0.281 768 Planarity : 0.004 0.036 890 Dihedral : 6.221 53.034 741 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.36 % Allowed : 16.88 % Favored : 80.76 % 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: -1.92 (0.32), residues: 634 helix: -2.85 (0.70), residues: 41 sheet: -0.58 (0.33), residues: 236 loop : -1.57 (0.32), 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 0.025 0.001 PHE H 156 TYR 0.016 0.001 TYR B 421 ARG 0.003 0.000 ARG L 217 *********************** 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 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: H 90 ASP cc_start: 0.8556 (m-30) cc_final: 0.8174 (m-30) REVERT: B 383 SER cc_start: 0.8286 (t) cc_final: 0.8065 (p) REVERT: B 408 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6502 (ptm160) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.1895 time to fit residues: 17.0968 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.211514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.182154 restraints weight = 5981.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.180441 restraints weight = 11947.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181232 restraints weight = 9583.683| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5077 Z= 0.230 Angle : 0.600 7.902 6913 Z= 0.305 Chirality : 0.045 0.306 768 Planarity : 0.004 0.032 890 Dihedral : 6.253 56.706 741 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.18 % Allowed : 17.60 % Favored : 80.22 % 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: -1.80 (0.32), residues: 634 helix: -2.75 (0.71), residues: 41 sheet: -0.51 (0.33), residues: 234 loop : -1.48 (0.32), 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 0.023 0.002 PHE H 156 TYR 0.016 0.001 TYR H 155 ARG 0.003 0.000 ARG L 217 *********************** 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: 12 poor density : 56 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8333 (mmm) cc_final: 0.7740 (mmm) REVERT: L 27 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: H 90 ASP cc_start: 0.8436 (m-30) cc_final: 0.8068 (m-30) REVERT: B 383 SER cc_start: 0.8353 (t) cc_final: 0.8059 (p) REVERT: B 408 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6571 (ptm160) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.2079 time to fit residues: 17.3777 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.212769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167548 restraints weight = 6008.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167179 restraints weight = 4886.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167411 restraints weight = 4000.371| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5077 Z= 0.277 Angle : 0.613 7.163 6913 Z= 0.314 Chirality : 0.046 0.337 768 Planarity : 0.004 0.033 890 Dihedral : 6.362 59.092 741 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.54 % Allowed : 17.24 % Favored : 80.22 % 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: -1.82 (0.33), residues: 634 helix: -2.72 (0.72), residues: 41 sheet: -0.53 (0.33), residues: 234 loop : -1.49 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.022 0.001 PHE H 68 TYR 0.019 0.002 TYR B 396 ARG 0.003 0.000 ARG L 67 *********************** 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 : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8463 (mmm) cc_final: 0.7888 (mmm) REVERT: L 27 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8510 (mp10) REVERT: H 90 ASP cc_start: 0.8548 (m-30) cc_final: 0.8233 (m-30) REVERT: B 383 SER cc_start: 0.8379 (t) cc_final: 0.8051 (p) REVERT: B 408 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6754 (ptm160) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.1803 time to fit residues: 16.5148 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 : 0.516 ------------------------------------------------------------------------------- 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 11 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.215773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184051 restraints weight = 6054.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181912 restraints weight = 10590.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183683 restraints weight = 9630.459| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5077 Z= 0.190 Angle : 0.586 6.868 6913 Z= 0.300 Chirality : 0.045 0.286 768 Planarity : 0.004 0.032 890 Dihedral : 6.136 59.269 741 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.18 % Allowed : 18.15 % 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: -1.76 (0.33), residues: 634 helix: -2.71 (0.71), residues: 41 sheet: -0.44 (0.33), residues: 234 loop : -1.49 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.008 0.001 HIS H 35 PHE 0.019 0.001 PHE H 68 TYR 0.017 0.001 TYR B 421 ARG 0.003 0.000 ARG L 217 ********************** 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 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: H 90 ASP cc_start: 0.8566 (m-30) cc_final: 0.8279 (m-30) REVERT: H 220 LYS cc_start: 0.7116 (tmtt) cc_final: 0.6726 (tmtt) REVERT: B 408 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6658 (ptm160) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.2006 time to fit residues: 17.2649 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 : 0.558 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.209963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160458 restraints weight = 6121.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162102 restraints weight = 5198.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162910 restraints weight = 4608.417| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 5077 Z= 0.392 Angle : 0.664 6.568 6913 Z= 0.344 Chirality : 0.047 0.371 768 Planarity : 0.005 0.035 890 Dihedral : 6.496 56.907 741 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.00 % Allowed : 18.69 % Favored : 79.31 % 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: -1.92 (0.33), residues: 634 helix: -2.78 (0.70), residues: 41 sheet: -0.58 (0.33), residues: 234 loop : -1.57 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.028 0.002 PHE H 68 TYR 0.021 0.002 TYR B 396 ARG 0.005 0.001 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.88 seconds wall clock time: 45 minutes 11.25 seconds (2711.25 seconds total)