Starting phenix.real_space_refine on Fri Dec 27 13:23:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eng_31210/12_2024/7eng_31210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eng_31210/12_2024/7eng_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_31210/12_2024/7eng_31210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eng_31210/12_2024/7eng_31210.map" model { file = "/net/cci-nas-00/data/ceres_data/7eng_31210/12_2024/7eng_31210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eng_31210/12_2024/7eng_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-5532/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: 4.36, per 1000 atoms: 0.88 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: 1.39 Conformation dependent library (CDL) restraints added in 658.4 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: 0.62 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: 1.30 Time building geometry restraints manager: 1.47 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: 6.920 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 16.250 Find NCS groups from input model: 0.080 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- 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 : 0.526 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: 0.2336 time to fit residues: 24.9063 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 : 0.593 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7288 (p90) cc_final: 0.7063 (p90) REVERT: H 90 ASP cc_start: 0.8587 (m-30) cc_final: 0.8362 (m-30) REVERT: B 383 SER cc_start: 0.8223 (t) cc_final: 0.8010 (p) outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.2221 time to fit residues: 20.9458 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 : 0.899 ------------------------------------------------------------------------------- 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 31 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 10.0000 chunk 56 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5077 Z= 0.240 Angle : 0.636 8.339 6913 Z= 0.321 Chirality : 0.046 0.337 768 Planarity : 0.004 0.035 890 Dihedral : 9.199 59.029 741 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.09 % Allowed : 13.07 % 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: -3.16 (0.74), residues: 35 sheet: -0.81 (0.32), residues: 247 loop : -1.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.020 0.001 PHE H 156 TYR 0.019 0.002 TYR H 155 ARG 0.004 0.000 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 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 146 TYR cc_start: 0.8351 (t80) cc_final: 0.8072 (t80) REVERT: H 53 TYR cc_start: 0.7267 (p90) cc_final: 0.7017 (p90) REVERT: H 90 ASP cc_start: 0.8552 (m-30) cc_final: 0.8317 (m-30) REVERT: B 383 SER cc_start: 0.8294 (t) cc_final: 0.8059 (p) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.2214 time to fit residues: 20.9029 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 5077 Z= 0.503 Angle : 0.752 8.951 6913 Z= 0.385 Chirality : 0.049 0.429 768 Planarity : 0.005 0.046 890 Dihedral : 8.089 46.652 741 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.00 % Allowed : 15.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.14 (0.76), residues: 34 sheet: -0.89 (0.33), residues: 241 loop : -1.70 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.006 0.002 HIS H 35 PHE 0.015 0.002 PHE L 124 TYR 0.022 0.003 TYR L 55 ARG 0.004 0.001 ARG H 72 *********************** 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 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7376 (p90) cc_final: 0.7119 (p90) REVERT: H 90 ASP cc_start: 0.8625 (m-30) cc_final: 0.8356 (m-30) REVERT: B 383 SER cc_start: 0.8334 (t) cc_final: 0.8105 (p) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.1987 time to fit residues: 19.7229 Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 99 ASP Chi-restraints excluded: chain B residue 395 VAL 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 34 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5077 Z= 0.209 Angle : 0.635 9.462 6913 Z= 0.319 Chirality : 0.046 0.339 768 Planarity : 0.004 0.037 890 Dihedral : 7.066 44.997 741 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.72 % Allowed : 15.97 % Favored : 81.31 % 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: -2.14 (0.32), residues: 634 helix: -3.14 (0.65), residues: 41 sheet: -0.76 (0.33), residues: 234 loop : -1.68 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.023 0.001 PHE H 156 TYR 0.019 0.001 TYR H 155 ARG 0.004 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 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7320 (p90) cc_final: 0.7102 (p90) REVERT: H 90 ASP cc_start: 0.8555 (m-30) cc_final: 0.8301 (m-30) REVERT: B 383 SER cc_start: 0.8304 (t) cc_final: 0.8059 (p) REVERT: B 408 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6595 (ptm160) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.2112 time to fit residues: 21.0787 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.0000 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5077 Z= 0.321 Angle : 0.650 8.108 6913 Z= 0.331 Chirality : 0.046 0.357 768 Planarity : 0.004 0.039 890 Dihedral : 6.814 44.982 741 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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: -2.11 (0.32), residues: 634 helix: -2.97 (0.69), residues: 41 sheet: -0.74 (0.33), residues: 234 loop : -1.68 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.008 0.002 HIS H 35 PHE 0.013 0.001 PHE L 124 TYR 0.018 0.002 TYR H 155 ARG 0.004 0.001 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 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: H 53 TYR cc_start: 0.7386 (p90) cc_final: 0.7148 (p90) REVERT: H 90 ASP cc_start: 0.8607 (m-30) cc_final: 0.8349 (m-30) REVERT: B 383 SER cc_start: 0.8341 (t) cc_final: 0.8068 (p) REVERT: B 408 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6603 (ptm160) REVERT: B 420 ASP cc_start: 0.7483 (p0) cc_final: 0.7282 (p0) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.1821 time to fit residues: 16.3927 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 : 0.570 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5077 Z= 0.286 Angle : 0.635 7.426 6913 Z= 0.323 Chirality : 0.046 0.361 768 Planarity : 0.004 0.039 890 Dihedral : 6.550 45.274 741 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % 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 : 0.17 % 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: -2.08 (0.32), residues: 634 helix: -2.91 (0.70), residues: 41 sheet: -0.73 (0.33), residues: 234 loop : -1.64 (0.32), 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 0.026 0.002 PHE H 156 TYR 0.016 0.002 TYR H 155 ARG 0.006 0.001 ARG B 355 *********************** 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 : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: H 53 TYR cc_start: 0.7311 (p90) cc_final: 0.7092 (p90) REVERT: H 90 ASP cc_start: 0.8561 (m-30) cc_final: 0.8350 (m-30) REVERT: B 383 SER cc_start: 0.8340 (t) cc_final: 0.8065 (p) REVERT: B 408 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6628 (ptm160) REVERT: B 420 ASP cc_start: 0.7443 (p0) cc_final: 0.7172 (p0) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.2450 time to fit residues: 21.9377 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 : 0.660 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 5077 Z= 0.379 Angle : 0.673 7.082 6913 Z= 0.345 Chirality : 0.047 0.385 768 Planarity : 0.004 0.040 890 Dihedral : 6.542 43.465 741 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % 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: -2.19 (0.32), residues: 634 helix: -2.92 (0.70), residues: 41 sheet: -0.83 (0.33), residues: 234 loop : -1.72 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.007 0.001 HIS H 35 PHE 0.015 0.002 PHE L 124 TYR 0.018 0.002 TYR L 55 ARG 0.006 0.001 ARG B 355 *********************** 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 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: H 53 TYR cc_start: 0.7266 (p90) cc_final: 0.7042 (p90) REVERT: H 90 ASP cc_start: 0.8639 (m-30) cc_final: 0.8385 (m-30) REVERT: B 383 SER cc_start: 0.8352 (t) cc_final: 0.8077 (p) REVERT: B 408 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6767 (ptm160) REVERT: B 420 ASP cc_start: 0.7425 (p0) cc_final: 0.7132 (p0) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.2293 time to fit residues: 21.5347 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 : 0.557 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5077 Z= 0.257 Angle : 0.629 7.032 6913 Z= 0.320 Chirality : 0.046 0.352 768 Planarity : 0.004 0.039 890 Dihedral : 6.263 43.755 741 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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 : 0.17 % 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: -2.14 (0.32), residues: 634 helix: -2.84 (0.71), residues: 41 sheet: -0.82 (0.33), residues: 236 loop : -1.67 (0.32), residues: 357 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 0.027 0.001 PHE H 156 TYR 0.016 0.002 TYR L 55 ARG 0.006 0.001 ARG B 355 *********************** 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 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8436 (mp10) REVERT: H 53 TYR cc_start: 0.7235 (p90) cc_final: 0.7016 (p90) REVERT: H 90 ASP cc_start: 0.8631 (m-30) cc_final: 0.8373 (m-30) REVERT: B 383 SER cc_start: 0.8339 (t) cc_final: 0.8064 (p) REVERT: B 408 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6620 (ptm160) REVERT: B 420 ASP cc_start: 0.7432 (p0) cc_final: 0.7179 (p0) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.2417 time to fit residues: 21.5703 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 : 0.567 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2627 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= 0.195 Angle : 0.596 6.471 6913 Z= 0.303 Chirality : 0.045 0.282 768 Planarity : 0.004 0.039 890 Dihedral : 5.900 47.940 741 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.00 % Allowed : 17.79 % 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: -2.04 (0.32), residues: 634 helix: -2.74 (0.73), residues: 41 sheet: -0.75 (0.32), residues: 236 loop : -1.60 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.008 0.001 HIS H 35 PHE 0.011 0.001 PHE L 124 TYR 0.014 0.001 TYR B 421 ARG 0.004 0.000 ARG L 60 ********************** 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 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: H 90 ASP cc_start: 0.8612 (m-30) cc_final: 0.8361 (m-30) REVERT: H 156 PHE cc_start: 0.7243 (t80) cc_final: 0.7037 (t80) REVERT: B 383 SER cc_start: 0.8358 (t) cc_final: 0.8071 (p) REVERT: B 408 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6562 (ptm160) REVERT: B 420 ASP cc_start: 0.7347 (p0) cc_final: 0.7090 (p0) REVERT: B 471 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7709 (mm-30) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.2140 time to fit residues: 19.3923 Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 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 13 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.0060 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.213049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175815 restraints weight = 5839.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168631 restraints weight = 6732.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170339 restraints weight = 7116.304| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2786 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= 0.169 Angle : 0.589 6.288 6913 Z= 0.300 Chirality : 0.045 0.290 768 Planarity : 0.004 0.039 890 Dihedral : 5.936 54.216 741 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.72 % Allowed : 17.06 % 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: -1.94 (0.32), residues: 634 helix: -2.71 (0.72), residues: 41 sheet: -0.67 (0.32), residues: 236 loop : -1.55 (0.33), residues: 357 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 0.015 0.001 PHE H 68 TYR 0.019 0.001 TYR B 421 ARG 0.004 0.000 ARG L 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.20 seconds wall clock time: 31 minutes 21.19 seconds (1881.19 seconds total)