Starting phenix.real_space_refine on Mon Sep 23 18:40:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/09_2024/7kwz_23059.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/09_2024/7kwz_23059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/09_2024/7kwz_23059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/09_2024/7kwz_23059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/09_2024/7kwz_23059.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/09_2024/7kwz_23059.cif" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 2770 2.51 5 N 895 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4695 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.28, per 1000 atoms: 0.49 Number of scatterers: 4695 At special positions: 0 Unit cell: (94.392, 91.08, 52.992, 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 50 16.00 O 980 8.00 N 895 7.00 C 2770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 814.9 milliseconds 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 865 1.31 - 1.43: 1405 1.43 - 1.56: 2415 1.56 - 1.68: 0 1.68 - 1.80: 100 Bond restraints: 4785 Sorted by residual: bond pdb=" CB ASN D 319 " pdb=" CG ASN D 319 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.82e+00 bond pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.76e+00 bond pdb=" CB ASN C 319 " pdb=" CG ASN C 319 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.70e+00 bond pdb=" CB ASN E 319 " pdb=" CG ASN E 319 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.65e+00 bond pdb=" CB ASN B 319 " pdb=" CG ASN B 319 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.65e+00 ... (remaining 4780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 5842 1.28 - 2.55: 425 2.55 - 3.83: 78 3.83 - 5.11: 25 5.11 - 6.38: 15 Bond angle restraints: 6385 Sorted by residual: angle pdb=" C MET D 336 " pdb=" N MET D 337 " pdb=" CA MET D 337 " ideal model delta sigma weight residual 122.17 117.93 4.24 1.54e+00 4.22e-01 7.57e+00 angle pdb=" C MET C 336 " pdb=" N MET C 337 " pdb=" CA MET C 337 " ideal model delta sigma weight residual 122.17 117.96 4.21 1.54e+00 4.22e-01 7.47e+00 angle pdb=" C MET A 336 " pdb=" N MET A 337 " pdb=" CA MET A 337 " ideal model delta sigma weight residual 122.17 117.99 4.18 1.54e+00 4.22e-01 7.36e+00 angle pdb=" C MET B 336 " pdb=" N MET B 337 " pdb=" CA MET B 337 " ideal model delta sigma weight residual 122.17 117.99 4.18 1.54e+00 4.22e-01 7.36e+00 angle pdb=" C MET E 336 " pdb=" N MET E 337 " pdb=" CA MET E 337 " ideal model delta sigma weight residual 122.17 118.01 4.16 1.54e+00 4.22e-01 7.31e+00 ... (remaining 6380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.30: 2119 9.30 - 18.60: 281 18.60 - 27.90: 181 27.90 - 37.20: 59 37.20 - 46.50: 15 Dihedral angle restraints: 2655 sinusoidal: 940 harmonic: 1715 Sorted by residual: dihedral pdb=" CA MET C 337 " pdb=" C MET C 337 " pdb=" N GLY C 338 " pdb=" CA GLY C 338 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA MET E 337 " pdb=" C MET E 337 " pdb=" N GLY E 338 " pdb=" CA GLY E 338 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA MET A 337 " pdb=" C MET A 337 " pdb=" N GLY A 338 " pdb=" CA GLY A 338 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 251 0.027 - 0.054: 167 0.054 - 0.081: 57 0.081 - 0.108: 37 0.108 - 0.135: 23 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA ILE C 318 " pdb=" N ILE C 318 " pdb=" C ILE C 318 " pdb=" CB ILE C 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 532 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 319 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C ASN D 319 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN D 319 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO D 320 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 319 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ASN E 319 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN E 319 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO E 320 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 319 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C ASN A 319 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN A 319 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO A 320 " -0.007 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1365 2.80 - 3.32: 4508 3.32 - 3.85: 8023 3.85 - 4.37: 9905 4.37 - 4.90: 19033 Nonbonded interactions: 42834 Sorted by model distance: nonbonded pdb=" O ASN C 279 " pdb=" OD1 ASN D 279 " model vdw 2.271 3.040 nonbonded pdb=" O ASN D 279 " pdb=" OD1 ASN E 279 " model vdw 2.276 3.040 nonbonded pdb=" O ASN B 279 " pdb=" OD1 ASN C 279 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 279 " pdb=" OD1 ASN B 279 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 374 " pdb=" O GLY C 351 " model vdw 2.310 3.040 ... (remaining 42829 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.006 0.060 4785 Z= 0.299 Angle : 0.804 6.384 6385 Z= 0.436 Chirality : 0.048 0.135 535 Planarity : 0.003 0.027 940 Dihedral : 12.477 46.502 1635 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.51 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.11), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 412 PHE 0.008 0.002 PHE D 401 TYR 0.007 0.002 TYR C 374 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7138 (mmp-170) REVERT: A 359 MET cc_start: 0.5447 (tpt) cc_final: 0.5232 (tpt) REVERT: A 360 GLN cc_start: 0.6244 (mt0) cc_final: 0.5871 (tp40) REVERT: B 359 MET cc_start: 0.5465 (tpt) cc_final: 0.5257 (tpt) REVERT: B 365 GLN cc_start: 0.6936 (mp10) cc_final: 0.6718 (mp10) REVERT: C 359 MET cc_start: 0.5600 (tpt) cc_final: 0.5272 (tpt) REVERT: D 359 MET cc_start: 0.5454 (tpt) cc_final: 0.5232 (tpt) REVERT: E 293 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7229 (pmt-80) REVERT: E 307 MET cc_start: 0.8057 (ttt) cc_final: 0.7815 (ttm) REVERT: E 365 GLN cc_start: 0.7579 (mp10) cc_final: 0.7372 (mp10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1594 time to fit residues: 25.6426 Evaluate side-chains 78 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 291 ASN B 319 ASN B 344 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 344 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 ASN ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 ASN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4785 Z= 0.148 Angle : 0.680 7.285 6385 Z= 0.349 Chirality : 0.044 0.123 535 Planarity : 0.003 0.050 940 Dihedral : 5.370 22.667 705 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.50 % Allowed : 10.68 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.39 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 385 PHE 0.008 0.001 PHE B 283 TYR 0.004 0.001 TYR E 374 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7095 (mmp-170) REVERT: A 303 GLN cc_start: 0.7010 (mt0) cc_final: 0.6497 (tm-30) REVERT: A 362 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 365 GLN cc_start: 0.7268 (mp10) cc_final: 0.6971 (mp10) REVERT: B 293 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7682 (mtp-110) REVERT: C 359 MET cc_start: 0.5432 (tpt) cc_final: 0.5209 (tpt) REVERT: C 360 GLN cc_start: 0.4764 (tt0) cc_final: 0.4523 (tm-30) REVERT: C 365 GLN cc_start: 0.6486 (mp10) cc_final: 0.5987 (mp10) REVERT: E 293 ARG cc_start: 0.8381 (mtp180) cc_final: 0.7245 (pmt-80) REVERT: E 307 MET cc_start: 0.8071 (ttt) cc_final: 0.7806 (ttm) REVERT: E 360 GLN cc_start: 0.5360 (tt0) cc_final: 0.5081 (tm-30) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.1867 time to fit residues: 25.1966 Evaluate side-chains 94 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4785 Z= 0.233 Angle : 0.710 6.706 6385 Z= 0.365 Chirality : 0.045 0.120 535 Planarity : 0.004 0.044 940 Dihedral : 5.507 26.613 705 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 4.09 % Allowed : 13.18 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.36 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 PHE 0.014 0.001 PHE B 283 TYR 0.008 0.002 TYR B 374 ARG 0.002 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7097 (mmp-170) REVERT: C 365 GLN cc_start: 0.6466 (mp10) cc_final: 0.5811 (mp10) REVERT: D 303 GLN cc_start: 0.6926 (mt0) cc_final: 0.6595 (tm-30) REVERT: D 323 MET cc_start: 0.7989 (mtp) cc_final: 0.7391 (mtp) REVERT: D 365 GLN cc_start: 0.7051 (mp10) cc_final: 0.6805 (mp10) REVERT: E 293 ARG cc_start: 0.8375 (mtp180) cc_final: 0.7199 (pmt-80) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.1738 time to fit residues: 23.6433 Evaluate side-chains 99 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4785 Z= 0.316 Angle : 0.787 6.927 6385 Z= 0.407 Chirality : 0.046 0.126 535 Planarity : 0.004 0.046 940 Dihedral : 5.749 28.289 705 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.86 % Allowed : 17.27 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.39 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 412 PHE 0.017 0.002 PHE B 283 TYR 0.010 0.002 TYR B 374 ARG 0.002 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.521 Fit side-chains REVERT: A 293 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7135 (mmp-170) REVERT: A 303 GLN cc_start: 0.7129 (mt0) cc_final: 0.6575 (tm-30) REVERT: A 362 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 365 GLN cc_start: 0.7596 (mp10) cc_final: 0.7392 (mp10) REVERT: A 406 ASP cc_start: 0.7806 (t0) cc_final: 0.7564 (m-30) REVERT: B 362 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 365 GLN cc_start: 0.7139 (mp10) cc_final: 0.6819 (mp10) REVERT: C 303 GLN cc_start: 0.7043 (mt0) cc_final: 0.6818 (tm-30) REVERT: C 354 GLN cc_start: 0.7792 (mp10) cc_final: 0.7092 (mp10) REVERT: C 359 MET cc_start: 0.4940 (tpt) cc_final: 0.3501 (mmp) REVERT: C 365 GLN cc_start: 0.6508 (mp10) cc_final: 0.5763 (mp10) REVERT: D 293 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7621 (mtp-110) REVERT: D 303 GLN cc_start: 0.7034 (mt0) cc_final: 0.6628 (tm-30) REVERT: D 323 MET cc_start: 0.7901 (mtp) cc_final: 0.7388 (mtp) REVERT: D 406 ASP cc_start: 0.7793 (m-30) cc_final: 0.7460 (t0) REVERT: E 293 ARG cc_start: 0.8370 (mtp180) cc_final: 0.7117 (pmt-80) REVERT: E 307 MET cc_start: 0.8113 (ttt) cc_final: 0.7814 (ttm) REVERT: E 354 GLN cc_start: 0.8418 (mp10) cc_final: 0.8217 (mp10) outliers start: 17 outliers final: 15 residues processed: 107 average time/residue: 0.1744 time to fit residues: 23.4540 Evaluate side-chains 108 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.0040 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4785 Z= 0.195 Angle : 0.690 6.174 6385 Z= 0.354 Chirality : 0.043 0.118 535 Planarity : 0.004 0.049 940 Dihedral : 5.245 25.038 705 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.41 % Allowed : 18.86 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.32 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 385 PHE 0.011 0.001 PHE B 283 TYR 0.006 0.001 TYR B 374 ARG 0.002 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.434 Fit side-chains REVERT: A 293 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7134 (mmp-170) REVERT: A 303 GLN cc_start: 0.7104 (mt0) cc_final: 0.6715 (tm-30) REVERT: A 319 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7369 (p0) REVERT: B 303 GLN cc_start: 0.6867 (tm-30) cc_final: 0.5769 (tm-30) REVERT: B 365 GLN cc_start: 0.7066 (mp10) cc_final: 0.6858 (mp10) REVERT: C 303 GLN cc_start: 0.6937 (mt0) cc_final: 0.6707 (tm-30) REVERT: C 362 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 365 GLN cc_start: 0.6501 (mp10) cc_final: 0.5457 (mp10) REVERT: D 293 ARG cc_start: 0.7692 (mtp-110) cc_final: 0.7359 (mtp-110) REVERT: D 303 GLN cc_start: 0.7027 (mt0) cc_final: 0.6657 (tm-30) REVERT: D 323 MET cc_start: 0.7902 (mtp) cc_final: 0.7513 (mtp) REVERT: D 406 ASP cc_start: 0.7799 (m-30) cc_final: 0.7327 (t0) REVERT: E 293 ARG cc_start: 0.8427 (mtp180) cc_final: 0.7117 (pmt-80) REVERT: E 307 MET cc_start: 0.8111 (ttt) cc_final: 0.7811 (ttm) REVERT: E 354 GLN cc_start: 0.8409 (mp10) cc_final: 0.8148 (mp10) REVERT: E 359 MET cc_start: 0.5824 (tpt) cc_final: 0.3544 (tmm) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.1855 time to fit residues: 25.5027 Evaluate side-chains 107 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4785 Z= 0.261 Angle : 0.743 7.814 6385 Z= 0.382 Chirality : 0.044 0.121 535 Planarity : 0.005 0.050 940 Dihedral : 5.422 26.586 705 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 4.09 % Allowed : 17.50 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.40 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 412 PHE 0.014 0.002 PHE B 283 TYR 0.008 0.002 TYR B 374 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.490 Fit side-chains REVERT: A 293 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7167 (mmp-170) REVERT: A 303 GLN cc_start: 0.7128 (mt0) cc_final: 0.6529 (tm-30) REVERT: A 319 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.7479 (p0) REVERT: A 362 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 414 MET cc_start: 0.5833 (mmm) cc_final: 0.4018 (mpp) REVERT: B 303 GLN cc_start: 0.6896 (tm-30) cc_final: 0.6023 (tm-30) REVERT: B 322 MET cc_start: 0.8094 (ptp) cc_final: 0.7622 (ptt) REVERT: C 303 GLN cc_start: 0.6987 (mt0) cc_final: 0.6783 (tm-30) REVERT: C 354 GLN cc_start: 0.7720 (mp10) cc_final: 0.7178 (mp10) REVERT: C 362 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7763 (tm-30) REVERT: C 365 GLN cc_start: 0.6513 (mp10) cc_final: 0.5489 (mp10) REVERT: D 293 ARG cc_start: 0.7683 (mtp-110) cc_final: 0.7344 (mtp-110) REVERT: D 303 GLN cc_start: 0.7071 (mt0) cc_final: 0.6665 (tm-30) REVERT: D 323 MET cc_start: 0.7922 (mtp) cc_final: 0.7575 (mtp) REVERT: D 405 MET cc_start: 0.6521 (tpt) cc_final: 0.6235 (tpt) REVERT: D 406 ASP cc_start: 0.7709 (m-30) cc_final: 0.7374 (t0) REVERT: E 293 ARG cc_start: 0.8455 (mtp180) cc_final: 0.7118 (pmt-80) REVERT: E 303 GLN cc_start: 0.7494 (tm-30) cc_final: 0.6745 (tm-30) REVERT: E 307 MET cc_start: 0.8129 (ttt) cc_final: 0.7835 (ttm) REVERT: E 356 GLN cc_start: 0.8255 (mp10) cc_final: 0.8051 (mp10) REVERT: E 359 MET cc_start: 0.5908 (tpt) cc_final: 0.3610 (tmm) REVERT: E 405 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6796 (ptp) outliers start: 18 outliers final: 14 residues processed: 110 average time/residue: 0.1818 time to fit residues: 25.1329 Evaluate side-chains 109 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 62 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4785 Z= 0.140 Angle : 0.667 7.013 6385 Z= 0.342 Chirality : 0.043 0.131 535 Planarity : 0.005 0.051 940 Dihedral : 4.937 21.826 705 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.32 % Allowed : 17.73 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.35 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 385 PHE 0.019 0.001 PHE E 289 TYR 0.004 0.001 TYR B 374 ARG 0.004 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.438 Fit side-chains REVERT: A 293 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7075 (mmp-170) REVERT: A 303 GLN cc_start: 0.7084 (mt0) cc_final: 0.6730 (tm-30) REVERT: A 319 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.7298 (p0) REVERT: A 336 MET cc_start: 0.7662 (mpp) cc_final: 0.7229 (mtt) REVERT: A 362 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 414 MET cc_start: 0.5743 (mmm) cc_final: 0.3919 (mpp) REVERT: B 303 GLN cc_start: 0.6871 (tm-30) cc_final: 0.5690 (tm-30) REVERT: B 307 MET cc_start: 0.7586 (ttt) cc_final: 0.7221 (ttm) REVERT: B 322 MET cc_start: 0.8089 (ptp) cc_final: 0.7652 (ptt) REVERT: C 303 GLN cc_start: 0.6866 (mt0) cc_final: 0.6663 (tm-30) REVERT: C 354 GLN cc_start: 0.7617 (mp10) cc_final: 0.7117 (mp10) REVERT: C 362 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 303 GLN cc_start: 0.6989 (mt0) cc_final: 0.6692 (tm-30) REVERT: D 323 MET cc_start: 0.7853 (mtp) cc_final: 0.7514 (mtp) REVERT: E 293 ARG cc_start: 0.8462 (mtp180) cc_final: 0.7124 (pmt-80) REVERT: E 303 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7052 (tm-30) REVERT: E 307 MET cc_start: 0.8107 (ttt) cc_final: 0.7820 (ttm) REVERT: E 359 MET cc_start: 0.5572 (tpt) cc_final: 0.3389 (tmm) REVERT: E 405 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6895 (ptp) outliers start: 19 outliers final: 14 residues processed: 105 average time/residue: 0.1535 time to fit residues: 20.7773 Evaluate side-chains 101 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4785 Z= 0.203 Angle : 0.728 7.936 6385 Z= 0.374 Chirality : 0.043 0.120 535 Planarity : 0.004 0.053 940 Dihedral : 5.071 23.483 705 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.09 % Allowed : 18.41 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.37 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 PHE 0.017 0.001 PHE E 289 TYR 0.006 0.001 TYR B 374 ARG 0.004 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.502 Fit side-chains REVERT: A 293 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7079 (mmp-170) REVERT: A 303 GLN cc_start: 0.7128 (mt0) cc_final: 0.6539 (tm-30) REVERT: A 319 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.7417 (p0) REVERT: A 336 MET cc_start: 0.7586 (mpp) cc_final: 0.7261 (mtt) REVERT: A 414 MET cc_start: 0.5808 (mmm) cc_final: 0.3983 (mpp) REVERT: B 303 GLN cc_start: 0.6906 (tm-30) cc_final: 0.5954 (tm-30) REVERT: B 307 MET cc_start: 0.7567 (ttt) cc_final: 0.7208 (ttm) REVERT: B 322 MET cc_start: 0.8100 (ptp) cc_final: 0.7594 (ptt) REVERT: C 354 GLN cc_start: 0.7641 (mp10) cc_final: 0.7015 (mp10) REVERT: C 362 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7627 (tm-30) REVERT: D 303 GLN cc_start: 0.7060 (mt0) cc_final: 0.6666 (tm-30) REVERT: D 323 MET cc_start: 0.7827 (mtp) cc_final: 0.7524 (mtp) REVERT: D 362 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8022 (tm-30) REVERT: E 293 ARG cc_start: 0.8484 (mtp180) cc_final: 0.7163 (pmt-80) REVERT: E 307 MET cc_start: 0.8129 (ttt) cc_final: 0.7810 (ttm) REVERT: E 322 MET cc_start: 0.8196 (ptt) cc_final: 0.7880 (ptt) REVERT: E 359 MET cc_start: 0.5663 (tpt) cc_final: 0.3332 (tmm) REVERT: E 405 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6840 (ptt) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 0.1655 time to fit residues: 21.5770 Evaluate side-chains 101 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4785 Z= 0.154 Angle : 0.714 8.690 6385 Z= 0.365 Chirality : 0.043 0.114 535 Planarity : 0.005 0.056 940 Dihedral : 4.827 21.926 705 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.64 % Allowed : 19.55 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.31 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 385 PHE 0.015 0.001 PHE E 289 TYR 0.004 0.001 TYR B 374 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.481 Fit side-chains REVERT: A 293 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7074 (mmp-170) REVERT: A 319 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7324 (p0) REVERT: A 336 MET cc_start: 0.7609 (mpp) cc_final: 0.7312 (mtt) REVERT: A 414 MET cc_start: 0.5773 (mmm) cc_final: 0.3957 (mpp) REVERT: B 303 GLN cc_start: 0.6815 (tm-30) cc_final: 0.6327 (tm-30) REVERT: B 307 MET cc_start: 0.7560 (ttt) cc_final: 0.7201 (ttm) REVERT: B 322 MET cc_start: 0.8139 (ptp) cc_final: 0.7637 (ptt) REVERT: B 365 GLN cc_start: 0.7098 (mp10) cc_final: 0.6852 (mp10) REVERT: C 354 GLN cc_start: 0.7628 (mp10) cc_final: 0.6983 (mp10) REVERT: C 362 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 303 GLN cc_start: 0.7072 (mt0) cc_final: 0.6627 (tm-30) REVERT: D 323 MET cc_start: 0.7788 (mtp) cc_final: 0.7517 (mtp) REVERT: E 293 ARG cc_start: 0.8498 (mtp180) cc_final: 0.7096 (pmt-80) REVERT: E 307 MET cc_start: 0.8132 (ttt) cc_final: 0.7828 (ttm) REVERT: E 322 MET cc_start: 0.8371 (ptt) cc_final: 0.8083 (ptp) REVERT: E 359 MET cc_start: 0.5546 (tpt) cc_final: 0.3333 (tmm) REVERT: E 405 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6860 (ptt) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.1630 time to fit residues: 21.6204 Evaluate side-chains 102 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4785 Z= 0.271 Angle : 0.810 9.614 6385 Z= 0.416 Chirality : 0.044 0.117 535 Planarity : 0.005 0.063 940 Dihedral : 5.311 25.807 705 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.64 % Allowed : 20.45 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.44 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 385 PHE 0.017 0.002 PHE E 289 TYR 0.008 0.002 TYR B 374 ARG 0.002 0.000 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.490 Fit side-chains REVERT: A 293 ARG cc_start: 0.8000 (mtp180) cc_final: 0.7185 (mmp-170) REVERT: A 303 GLN cc_start: 0.7073 (mt0) cc_final: 0.6466 (tm-30) REVERT: A 319 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 414 MET cc_start: 0.5818 (mmm) cc_final: 0.3985 (mpp) REVERT: B 303 GLN cc_start: 0.6805 (tm-30) cc_final: 0.6048 (tm-30) REVERT: B 365 GLN cc_start: 0.7148 (mp10) cc_final: 0.6845 (mp10) REVERT: C 362 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 303 GLN cc_start: 0.7109 (mt0) cc_final: 0.6613 (tm-30) REVERT: D 323 MET cc_start: 0.7920 (mtp) cc_final: 0.7604 (mtp) REVERT: D 362 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7938 (tm-30) REVERT: D 363 PRO cc_start: 0.8984 (Cg_exo) cc_final: 0.8743 (Cg_endo) REVERT: D 406 ASP cc_start: 0.7712 (m-30) cc_final: 0.7373 (t0) REVERT: E 293 ARG cc_start: 0.8482 (mtp180) cc_final: 0.7143 (pmt-80) REVERT: E 307 MET cc_start: 0.8213 (ttt) cc_final: 0.7903 (ttm) REVERT: E 322 MET cc_start: 0.8387 (ptt) cc_final: 0.8171 (ptp) REVERT: E 359 MET cc_start: 0.5735 (tpt) cc_final: 0.3435 (tmm) REVERT: E 405 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6746 (ptt) outliers start: 16 outliers final: 14 residues processed: 105 average time/residue: 0.1616 time to fit residues: 21.6444 Evaluate side-chains 106 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 405 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN D 312 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.140428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.098659 restraints weight = 5889.901| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.75 r_work: 0.3624 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4785 Z= 0.161 Angle : 0.756 9.542 6385 Z= 0.385 Chirality : 0.043 0.114 535 Planarity : 0.004 0.066 940 Dihedral : 4.906 22.062 705 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.09 % Allowed : 20.68 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.36 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 385 PHE 0.016 0.001 PHE D 289 TYR 0.004 0.001 TYR B 374 ARG 0.002 0.000 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.28 seconds wall clock time: 26 minutes 36.06 seconds (1596.06 seconds total)