Starting phenix.real_space_refine on Sun Mar 10 19:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/03_2024/7kwz_23059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/03_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_23059/03_2024/7kwz_23059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/03_2024/7kwz_23059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/03_2024/7kwz_23059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/03_2024/7kwz_23059.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4695 Number of models: 1 Model: "" Number of chains: 5 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} Chain: "B" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Time building chain proxies: 2.90, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.00 Conformation dependent library (CDL) restraints added in 866.1 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: 0.66 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: 2.10 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: 98.34 - 105.50: 110 105.50 - 112.66: 2018 112.66 - 119.82: 1558 119.82 - 126.99: 2635 126.99 - 134.15: 64 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 2.440 ... (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 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: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 1.880 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.710 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- 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 : 0.496 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: 0.1524 time to fit residues: 24.6773 Evaluate side-chains 78 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 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 331 GLN C 344 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 ASN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4785 Z= 0.112 Angle : 0.635 6.784 6385 Z= 0.323 Chirality : 0.043 0.113 535 Planarity : 0.003 0.045 940 Dihedral : 5.146 21.350 705 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.95 % Allowed : 9.32 % Favored : 87.73 % 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: -5.30 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 385 PHE 0.006 0.001 PHE B 283 TYR 0.002 0.000 TYR A 374 ARG 0.003 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 108 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.497 Fit side-chains REVERT: A 293 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7161 (mmp-170) REVERT: A 303 GLN cc_start: 0.6907 (mt0) cc_final: 0.6402 (tm-30) REVERT: A 359 MET cc_start: 0.5855 (tpt) cc_final: 0.5632 (tpt) REVERT: A 360 GLN cc_start: 0.6451 (mt0) cc_final: 0.5937 (tp40) REVERT: B 356 GLN cc_start: 0.8263 (mp10) cc_final: 0.7887 (mp10) REVERT: C 359 MET cc_start: 0.5198 (tpt) cc_final: 0.4995 (tpt) REVERT: D 360 GLN cc_start: 0.4905 (tt0) cc_final: 0.4628 (tm-30) REVERT: E 293 ARG cc_start: 0.8374 (mtp180) cc_final: 0.7232 (pmt-80) REVERT: E 307 MET cc_start: 0.8070 (ttt) cc_final: 0.7781 (ttm) REVERT: E 365 GLN cc_start: 0.7394 (mp10) cc_final: 0.7176 (mp10) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.1636 time to fit residues: 21.8338 Evaluate side-chains 87 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 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** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4785 Z= 0.237 Angle : 0.693 7.928 6385 Z= 0.354 Chirality : 0.044 0.125 535 Planarity : 0.004 0.044 940 Dihedral : 5.467 25.704 705 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 4.55 % Allowed : 12.73 % 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: -5.31 (0.16), 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 0.011 0.002 TRP A 412 PHE 0.014 0.002 PHE B 283 TYR 0.007 0.002 TYR B 374 ARG 0.004 0.001 ARG B 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 105 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7170 (mmp-170) REVERT: A 406 ASP cc_start: 0.7626 (m-30) cc_final: 0.7407 (t0) REVERT: B 293 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7623 (mtp-110) REVERT: C 356 GLN cc_start: 0.8355 (mp10) cc_final: 0.8051 (mp10) REVERT: C 359 MET cc_start: 0.4871 (tpt) cc_final: 0.3732 (mmp) REVERT: C 362 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 323 MET cc_start: 0.7971 (mtp) cc_final: 0.7375 (mtp) REVERT: E 293 ARG cc_start: 0.8351 (mtp180) cc_final: 0.7142 (pmt-80) REVERT: E 307 MET cc_start: 0.8154 (ttt) cc_final: 0.7857 (ttm) REVERT: E 359 MET cc_start: 0.5758 (tpt) cc_final: 0.3542 (tmm) REVERT: E 365 GLN cc_start: 0.7422 (mp10) cc_final: 0.7219 (mp10) outliers start: 20 outliers final: 17 residues processed: 98 average time/residue: 0.1634 time to fit residues: 20.2863 Evaluate side-chains 97 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 398 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 332 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 398 ASN 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: 7.9990 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 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** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4785 Z= 0.222 Angle : 0.679 6.657 6385 Z= 0.347 Chirality : 0.043 0.125 535 Planarity : 0.004 0.047 940 Dihedral : 5.337 25.485 705 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.00 % Allowed : 15.00 % Favored : 80.00 % 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: -5.26 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 412 PHE 0.012 0.001 PHE B 283 TYR 0.006 0.002 TYR B 374 ARG 0.002 0.000 ARG B 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 111 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7172 (mmp-170) REVERT: A 303 GLN cc_start: 0.7082 (mt0) cc_final: 0.6613 (tm-30) REVERT: A 362 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 406 ASP cc_start: 0.7688 (m-30) cc_final: 0.7331 (t0) REVERT: B 293 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: B 322 MET cc_start: 0.8124 (ptp) cc_final: 0.7619 (ptt) REVERT: B 406 ASP cc_start: 0.7452 (m-30) cc_final: 0.7169 (t0) REVERT: C 322 MET cc_start: 0.8191 (ptp) cc_final: 0.7744 (ptt) REVERT: C 359 MET cc_start: 0.4620 (tpt) cc_final: 0.3523 (mmp) REVERT: C 362 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 398 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8506 (m-40) REVERT: D 303 GLN cc_start: 0.7108 (mt0) cc_final: 0.6674 (tm-30) REVERT: D 323 MET cc_start: 0.7846 (mtp) cc_final: 0.7363 (mtp) REVERT: E 293 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7146 (pmt-80) REVERT: E 303 GLN cc_start: 0.7536 (tm-30) cc_final: 0.6704 (tm-30) REVERT: E 359 MET cc_start: 0.5787 (tpt) cc_final: 0.3539 (tmm) REVERT: E 365 GLN cc_start: 0.7440 (mp10) cc_final: 0.7232 (mp10) outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 0.1592 time to fit residues: 21.3457 Evaluate side-chains 102 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 398 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 398 ASN 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: 5.9990 chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 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** ** D 291 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: 0.7959 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4785 Z= 0.324 Angle : 0.756 7.400 6385 Z= 0.393 Chirality : 0.045 0.127 535 Planarity : 0.004 0.049 940 Dihedral : 5.723 27.861 705 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Rotamer: Outliers : 4.77 % Allowed : 17.27 % 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: -5.40 (0.16), 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 0.010 0.002 TRP E 412 PHE 0.017 0.002 PHE B 283 TYR 0.008 0.002 TYR B 374 ARG 0.001 0.000 ARG A 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 108 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7230 (mmp-170) REVERT: A 303 GLN cc_start: 0.7110 (mt0) cc_final: 0.6843 (tm-30) REVERT: A 406 ASP cc_start: 0.7815 (m-30) cc_final: 0.7443 (t0) REVERT: B 406 ASP cc_start: 0.7638 (m-30) cc_final: 0.7320 (t0) REVERT: B 414 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.4946 (mmm) REVERT: C 359 MET cc_start: 0.4773 (tpt) cc_final: 0.3538 (mmp) REVERT: C 362 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 398 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8607 (m-40) REVERT: D 303 GLN cc_start: 0.7091 (mt0) cc_final: 0.6529 (tm-30) REVERT: D 323 MET cc_start: 0.7926 (mtp) cc_final: 0.7523 (mtp) REVERT: D 406 ASP cc_start: 0.7858 (m-30) cc_final: 0.7524 (t0) REVERT: E 293 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7182 (pmt-80) REVERT: E 303 GLN cc_start: 0.7588 (tm-30) cc_final: 0.6633 (tm-30) REVERT: E 307 MET cc_start: 0.8185 (ttt) cc_final: 0.7904 (ttm) REVERT: E 359 MET cc_start: 0.5930 (tpt) cc_final: 0.3641 (tmm) outliers start: 21 outliers final: 17 residues processed: 101 average time/residue: 0.1727 time to fit residues: 22.1833 Evaluate side-chains 104 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 405 MET Chi-restraints excluded: chain E residue 414 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.0670 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 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** ** D 291 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: 0.7914 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4785 Z= 0.205 Angle : 0.686 6.906 6385 Z= 0.353 Chirality : 0.043 0.131 535 Planarity : 0.004 0.050 940 Dihedral : 5.348 25.547 705 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 5.00 % Allowed : 17.95 % Favored : 77.05 % 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: -5.38 (0.16), 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 0.002 TRP B 385 PHE 0.012 0.001 PHE B 283 TYR 0.005 0.001 TYR B 374 ARG 0.005 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 114 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7254 (mmp-170) REVERT: A 303 GLN cc_start: 0.7107 (mt0) cc_final: 0.6854 (tm-30) REVERT: A 362 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 406 ASP cc_start: 0.7718 (m-30) cc_final: 0.7389 (t0) REVERT: B 322 MET cc_start: 0.8133 (ptp) cc_final: 0.7644 (ptt) REVERT: B 356 GLN cc_start: 0.8200 (mp10) cc_final: 0.7991 (mp10) REVERT: B 406 ASP cc_start: 0.7556 (m-30) cc_final: 0.7300 (t0) REVERT: B 414 MET cc_start: 0.5577 (OUTLIER) cc_final: 0.4815 (mmm) REVERT: C 359 MET cc_start: 0.4673 (tpt) cc_final: 0.3465 (mmp) REVERT: C 362 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 398 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8559 (m-40) REVERT: D 303 GLN cc_start: 0.7094 (mt0) cc_final: 0.6673 (tm-30) REVERT: D 323 MET cc_start: 0.7876 (mtp) cc_final: 0.7541 (mtp) REVERT: E 293 ARG cc_start: 0.8389 (mtp180) cc_final: 0.7207 (pmt-80) REVERT: E 303 GLN cc_start: 0.7590 (tm-30) cc_final: 0.6574 (tm-30) REVERT: E 307 MET cc_start: 0.8209 (ttt) cc_final: 0.7936 (ttm) REVERT: E 359 MET cc_start: 0.5844 (tpt) cc_final: 0.3565 (tmm) outliers start: 22 outliers final: 16 residues processed: 107 average time/residue: 0.1683 time to fit residues: 22.7832 Evaluate side-chains 105 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 414 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.0970 chunk 35 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 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: 0.7931 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4785 Z= 0.227 Angle : 0.699 6.659 6385 Z= 0.362 Chirality : 0.044 0.137 535 Planarity : 0.004 0.052 940 Dihedral : 5.368 25.970 705 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 5.00 % Allowed : 19.55 % Favored : 75.45 % 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: -5.43 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 412 PHE 0.012 0.001 PHE B 283 TYR 0.006 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 113 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7222 (mmp-170) REVERT: A 303 GLN cc_start: 0.7115 (mt0) cc_final: 0.6853 (tm-30) REVERT: A 406 ASP cc_start: 0.7755 (m-30) cc_final: 0.7415 (t0) REVERT: B 356 GLN cc_start: 0.8169 (mp10) cc_final: 0.7933 (mp10) REVERT: B 406 ASP cc_start: 0.7621 (m-30) cc_final: 0.7326 (t0) REVERT: B 414 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.4849 (mmm) REVERT: C 359 MET cc_start: 0.4660 (tpt) cc_final: 0.3381 (mmp) REVERT: C 362 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 398 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (m-40) REVERT: D 303 GLN cc_start: 0.7085 (mt0) cc_final: 0.6667 (tm-30) REVERT: D 323 MET cc_start: 0.7909 (mtp) cc_final: 0.7610 (mtp) REVERT: D 406 ASP cc_start: 0.7816 (m-30) cc_final: 0.7460 (t0) REVERT: E 293 ARG cc_start: 0.8379 (mtp180) cc_final: 0.7189 (pmt-80) REVERT: E 303 GLN cc_start: 0.7618 (tm-30) cc_final: 0.6574 (tm-30) REVERT: E 307 MET cc_start: 0.8229 (ttt) cc_final: 0.7945 (ttm) REVERT: E 322 MET cc_start: 0.8421 (ptp) cc_final: 0.8160 (ptt) REVERT: E 359 MET cc_start: 0.5860 (tpt) cc_final: 0.3586 (tmm) outliers start: 22 outliers final: 15 residues processed: 109 average time/residue: 0.1658 time to fit residues: 23.0356 Evaluate side-chains 105 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 398 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 358 ASN D 291 ASN D 358 ASN E 319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4785 Z= 0.117 Angle : 0.629 6.329 6385 Z= 0.322 Chirality : 0.042 0.114 535 Planarity : 0.004 0.055 940 Dihedral : 4.738 21.715 705 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.95 % Allowed : 20.91 % Favored : 76.14 % 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: -5.25 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 385 PHE 0.011 0.001 PHE E 289 TYR 0.001 0.001 TYR E 374 ARG 0.007 0.001 ARG D 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 105 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7150 (mmp-170) REVERT: A 303 GLN cc_start: 0.7084 (mt0) cc_final: 0.6656 (tm-30) REVERT: A 336 MET cc_start: 0.7611 (mpp) cc_final: 0.7361 (mtt) REVERT: A 406 ASP cc_start: 0.7684 (m-30) cc_final: 0.7387 (t0) REVERT: B 322 MET cc_start: 0.7730 (ptp) cc_final: 0.7436 (ptt) REVERT: B 414 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.4905 (mmm) REVERT: C 359 MET cc_start: 0.4619 (tpt) cc_final: 0.3242 (mmp) REVERT: C 362 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 410 SER cc_start: 0.8328 (m) cc_final: 0.7411 (p) REVERT: D 303 GLN cc_start: 0.7030 (mt0) cc_final: 0.6570 (tm-30) REVERT: D 323 MET cc_start: 0.7871 (mtp) cc_final: 0.7554 (mtp) REVERT: D 336 MET cc_start: 0.7295 (mtt) cc_final: 0.7038 (mtt) REVERT: D 410 SER cc_start: 0.8313 (m) cc_final: 0.7440 (p) REVERT: E 293 ARG cc_start: 0.8405 (mtp180) cc_final: 0.7190 (pmt-80) REVERT: E 303 GLN cc_start: 0.7605 (tm-30) cc_final: 0.6725 (tm-30) REVERT: E 307 MET cc_start: 0.8220 (ttt) cc_final: 0.7948 (ttm) REVERT: E 322 MET cc_start: 0.8338 (ptp) cc_final: 0.8120 (ptt) REVERT: E 359 MET cc_start: 0.5597 (tpt) cc_final: 0.3278 (tmm) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.1638 time to fit residues: 21.1632 Evaluate side-chains 93 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain E residue 332 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 0.034 4785 Z= 0.182 Angle : 0.696 8.555 6385 Z= 0.357 Chirality : 0.043 0.121 535 Planarity : 0.004 0.059 940 Dihedral : 4.947 24.346 705 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.95 % Allowed : 20.45 % Favored : 76.59 % 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: -5.30 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 412 PHE 0.010 0.001 PHE A 283 TYR 0.004 0.001 TYR B 374 ARG 0.006 0.001 ARG D 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 100 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7176 (mmp-170) REVERT: A 303 GLN cc_start: 0.7062 (mt0) cc_final: 0.6603 (tm-30) REVERT: A 406 ASP cc_start: 0.7676 (m-30) cc_final: 0.7414 (t0) REVERT: B 337 MET cc_start: 0.7960 (ttp) cc_final: 0.7748 (ttp) REVERT: B 414 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4715 (mmm) REVERT: C 359 MET cc_start: 0.4553 (tpt) cc_final: 0.3326 (mmp) REVERT: C 362 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 410 SER cc_start: 0.8337 (m) cc_final: 0.7372 (p) REVERT: D 323 MET cc_start: 0.7928 (mtp) cc_final: 0.7623 (mtp) REVERT: D 410 SER cc_start: 0.8375 (m) cc_final: 0.7521 (p) REVERT: E 293 ARG cc_start: 0.8400 (mtp180) cc_final: 0.7193 (pmt-80) REVERT: E 303 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6826 (tm-30) REVERT: E 307 MET cc_start: 0.8229 (ttt) cc_final: 0.7945 (ttm) REVERT: E 322 MET cc_start: 0.8402 (ptp) cc_final: 0.8164 (ptt) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1581 time to fit residues: 19.6079 Evaluate side-chains 101 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 8.9990 chunk 59 optimal weight: 0.0000 chunk 51 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4785 Z= 0.199 Angle : 0.736 8.632 6385 Z= 0.376 Chirality : 0.044 0.120 535 Planarity : 0.005 0.062 940 Dihedral : 5.058 25.082 705 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.95 % Allowed : 20.91 % Favored : 76.14 % 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 (0.16), 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 0.008 0.001 TRP A 412 PHE 0.013 0.001 PHE A 283 TYR 0.004 0.001 TYR B 374 ARG 0.006 0.001 ARG D 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 103 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 293 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7173 (mmp-170) REVERT: A 303 GLN cc_start: 0.7084 (mt0) cc_final: 0.6622 (tm-30) REVERT: A 362 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 406 ASP cc_start: 0.7590 (m-30) cc_final: 0.7365 (t0) REVERT: B 307 MET cc_start: 0.7708 (ttt) cc_final: 0.7307 (ttm) REVERT: B 322 MET cc_start: 0.8417 (ptt) cc_final: 0.8030 (ptp) REVERT: B 414 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.4896 (mmm) REVERT: C 362 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 410 SER cc_start: 0.8412 (m) cc_final: 0.7457 (p) REVERT: D 323 MET cc_start: 0.7884 (mtp) cc_final: 0.7615 (mtp) REVERT: D 410 SER cc_start: 0.8405 (m) cc_final: 0.7568 (p) REVERT: E 293 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7189 (pmt-80) REVERT: E 303 GLN cc_start: 0.7458 (tm-30) cc_final: 0.6914 (tm-30) REVERT: E 307 MET cc_start: 0.8238 (ttt) cc_final: 0.7963 (ttm) REVERT: E 322 MET cc_start: 0.8414 (ptp) cc_final: 0.8129 (ptt) REVERT: E 359 MET cc_start: 0.5697 (tpt) cc_final: 0.3817 (tmm) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.1619 time to fit residues: 21.3543 Evaluate side-chains 102 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.133923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.090916 restraints weight = 6006.211| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.84 r_work: 0.3509 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 4785 Z= 0.404 Angle : 0.902 9.812 6385 Z= 0.467 Chirality : 0.048 0.159 535 Planarity : 0.005 0.065 940 Dihedral : 5.976 29.574 705 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.85 % Favored : 80.15 % Rotamer: Outliers : 3.41 % Allowed : 21.14 % Favored : 75.45 % 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: -5.58 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.12), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 412 PHE 0.024 0.002 PHE A 283 TYR 0.008 0.002 TYR B 374 ARG 0.005 0.001 ARG D 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.95 seconds wall clock time: 26 minutes 54.90 seconds (1614.90 seconds total)