Starting phenix.real_space_refine on Mon Sep 23 14:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/09_2024/8ber_16009.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/09_2024/8ber_16009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/09_2024/8ber_16009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/09_2024/8ber_16009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/09_2024/8ber_16009.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/09_2024/8ber_16009.cif" } resolution = 4.0 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= 0.079 sd= 0.328 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 18 5.16 5 C 2157 2.51 5 N 546 2.21 5 O 588 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: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 4.00, per 1000 atoms: 1.21 Number of scatterers: 3309 At special positions: 0 Unit cell: (94.095, 70.848, 81.918, 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 18 16.00 O 588 8.00 N 546 7.00 C 2157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 59 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 393.1 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 17 No H-bonds generated for 'chain 'A' and resid 16 through 17' Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.882A pdb=" N ARG A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.664A pdb=" N THR A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 232 through 250 removed outlier: 3.573A pdb=" N LYS A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 17 through 22 removed outlier: 6.190A pdb=" N ASP B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 47 through 73 Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.790A pdb=" N VAL B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 251 through 268 removed outlier: 4.230A pdb=" N THR B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 16 through 17 No H-bonds generated for 'chain 'C' and resid 16 through 17' Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.925A pdb=" N ARG C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ALA C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 224 through 251 removed outlier: 5.207A pdb=" N LEU C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 221 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1029 1.34 - 1.46: 694 1.46 - 1.57: 1661 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 3411 Sorted by residual: bond pdb=" CA ILE A 279 " pdb=" CB ILE A 279 " ideal model delta sigma weight residual 1.527 1.547 -0.021 1.31e-02 5.83e+03 2.45e+00 bond pdb=" CG MET C 64 " pdb=" SD MET C 64 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.45e+00 bond pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CG GLU C 257 " pdb=" CD GLU C 257 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.23e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 4591 2.16 - 4.32: 63 4.32 - 6.48: 7 6.48 - 8.64: 0 8.64 - 10.79: 1 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C TYR A 272 " pdb=" N ARG A 273 " pdb=" CA ARG A 273 " ideal model delta sigma weight residual 120.49 131.28 -10.79 1.42e+00 4.96e-01 5.78e+01 angle pdb=" N GLU C 257 " pdb=" CA GLU C 257 " pdb=" CB GLU C 257 " ideal model delta sigma weight residual 110.28 116.61 -6.33 1.55e+00 4.16e-01 1.67e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta sigma weight residual 110.28 116.25 -5.97 1.55e+00 4.16e-01 1.49e+01 angle pdb=" C ILE C 256 " pdb=" N GLU C 257 " pdb=" CA GLU C 257 " ideal model delta sigma weight residual 120.31 115.08 5.23 1.52e+00 4.33e-01 1.18e+01 angle pdb=" C ASN C 232 " pdb=" N MET C 233 " pdb=" CA MET C 233 " ideal model delta sigma weight residual 122.23 117.61 4.62 1.57e+00 4.06e-01 8.64e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 1709 11.96 - 23.92: 200 23.92 - 35.88: 62 35.88 - 47.85: 22 47.85 - 59.81: 8 Dihedral angle restraints: 2001 sinusoidal: 792 harmonic: 1209 Sorted by residual: dihedral pdb=" CA ILE B 266 " pdb=" C ILE B 266 " pdb=" N ARG B 267 " pdb=" CA ARG B 267 " ideal model delta harmonic sigma weight residual 180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 123.36 -30.36 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA ARG B 267 " pdb=" C ARG B 267 " pdb=" N THR B 268 " pdb=" CA THR B 268 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 452 0.056 - 0.112: 66 0.112 - 0.168: 4 0.168 - 0.224: 1 0.224 - 0.280: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB THR C 282 " pdb=" CA THR C 282 " pdb=" OG1 THR C 282 " pdb=" CG2 THR C 282 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 522 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 230 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C ASN C 230 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN C 230 " -0.017 2.00e-02 2.50e+03 pdb=" N THR C 231 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 269 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO B 270 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 273 " -0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO C 274 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 274 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 274 " -0.016 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 480 2.75 - 3.29: 3664 3.29 - 3.83: 5909 3.83 - 4.36: 6389 4.36 - 4.90: 10758 Nonbonded interactions: 27200 Sorted by model distance: nonbonded pdb=" O TYR C 228 " pdb=" ND2 ASN C 232 " model vdw 2.214 3.120 nonbonded pdb=" O VAL A 11 " pdb=" OG SER A 15 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASN C 230 " pdb=" N THR C 231 " model vdw 2.241 3.120 nonbonded pdb=" OE2 GLU A 6 " pdb=" NH1 ARG B 54 " model vdw 2.256 3.120 nonbonded pdb=" O VAL A 229 " pdb=" N GLY A 234 " model vdw 2.284 3.120 ... (remaining 27195 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.003 0.031 3411 Z= 0.192 Angle : 0.613 10.795 4662 Z= 0.352 Chirality : 0.041 0.280 525 Planarity : 0.004 0.042 585 Dihedral : 12.678 59.807 1212 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 2.47 (0.44), residues: 402 helix: 1.88 (0.31), residues: 294 sheet: None (None), residues: 0 loop : 1.18 (0.68), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 60 HIS 0.002 0.001 HIS B 49 PHE 0.013 0.001 PHE B 237 TYR 0.006 0.001 TYR A 272 ARG 0.007 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.580 Fit side-chains REVERT: A 64 MET cc_start: 0.9413 (mmp) cc_final: 0.9174 (mmt) REVERT: A 233 MET cc_start: 0.9353 (mpp) cc_final: 0.9003 (mpp) REVERT: B 64 MET cc_start: 0.9228 (mmp) cc_final: 0.8838 (mmt) REVERT: B 233 MET cc_start: 0.9501 (pmm) cc_final: 0.9161 (pmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1671 time to fit residues: 4.7217 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3411 Z= 0.216 Angle : 0.615 6.822 4662 Z= 0.334 Chirality : 0.042 0.276 525 Planarity : 0.005 0.041 585 Dihedral : 4.589 21.601 447 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: 2.56 (0.43), residues: 402 helix: 1.98 (0.30), residues: 297 sheet: None (None), residues: 0 loop : 1.08 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 69 HIS 0.003 0.001 HIS B 45 PHE 0.017 0.001 PHE B 237 TYR 0.008 0.001 TYR C 272 ARG 0.004 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.424 Fit side-chains REVERT: A 64 MET cc_start: 0.9438 (mmp) cc_final: 0.9182 (mmt) REVERT: A 233 MET cc_start: 0.9421 (mpp) cc_final: 0.9068 (mpp) REVERT: B 64 MET cc_start: 0.9312 (mmp) cc_final: 0.8880 (mmt) REVERT: C 64 MET cc_start: 0.9383 (mmp) cc_final: 0.9178 (mmt) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1430 time to fit residues: 2.6447 Evaluate side-chains 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3411 Z= 0.230 Angle : 0.579 5.580 4662 Z= 0.315 Chirality : 0.041 0.265 525 Planarity : 0.005 0.046 585 Dihedral : 4.680 22.297 447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 8.47 % Favored : 90.98 % 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: 2.58 (0.43), residues: 402 helix: 1.99 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 1.07 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 69 HIS 0.003 0.001 HIS B 45 PHE 0.010 0.002 PHE B 237 TYR 0.011 0.001 TYR B 228 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9452 (mmp) cc_final: 0.9188 (mmt) REVERT: A 233 MET cc_start: 0.9426 (mpp) cc_final: 0.9037 (mpp) REVERT: B 64 MET cc_start: 0.9328 (mmp) cc_final: 0.8892 (mmt) REVERT: C 64 MET cc_start: 0.9402 (mmp) cc_final: 0.9127 (mmt) REVERT: C 253 GLU cc_start: 0.9659 (pm20) cc_final: 0.9394 (pm20) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.1369 time to fit residues: 2.9345 Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3411 Z= 0.185 Angle : 0.569 7.896 4662 Z= 0.308 Chirality : 0.039 0.231 525 Planarity : 0.004 0.044 585 Dihedral : 4.594 22.179 447 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.82 % Allowed : 9.84 % Favored : 89.34 % 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: 2.66 (0.43), residues: 402 helix: 2.03 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 1.19 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.002 0.001 HIS A 244 PHE 0.008 0.001 PHE C 16 TYR 0.012 0.001 TYR B 228 ARG 0.004 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9454 (mmp) cc_final: 0.9184 (mmt) REVERT: A 233 MET cc_start: 0.9464 (mpp) cc_final: 0.9076 (mpp) REVERT: B 64 MET cc_start: 0.9336 (mmp) cc_final: 0.8944 (mmt) REVERT: C 64 MET cc_start: 0.9402 (mmp) cc_final: 0.9119 (mmt) REVERT: C 253 GLU cc_start: 0.9661 (pm20) cc_final: 0.9405 (pm20) outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.1225 time to fit residues: 2.7794 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3411 Z= 0.234 Angle : 0.585 6.882 4662 Z= 0.314 Chirality : 0.039 0.239 525 Planarity : 0.005 0.043 585 Dihedral : 4.600 22.467 447 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 11.20 % Favored : 87.98 % 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: 2.68 (0.43), residues: 402 helix: 2.07 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.08 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 69 HIS 0.004 0.001 HIS B 45 PHE 0.009 0.001 PHE A 21 TYR 0.012 0.001 TYR B 228 ARG 0.005 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9456 (mmp) cc_final: 0.9195 (mmt) REVERT: B 64 MET cc_start: 0.9369 (mmp) cc_final: 0.8956 (mmt) REVERT: C 64 MET cc_start: 0.9407 (mmp) cc_final: 0.9105 (mmm) outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.1355 time to fit residues: 2.8598 Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.0000 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3411 Z= 0.201 Angle : 0.578 9.397 4662 Z= 0.311 Chirality : 0.039 0.222 525 Planarity : 0.004 0.042 585 Dihedral : 4.535 22.501 447 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 12.57 % Favored : 86.89 % 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: 2.73 (0.43), residues: 402 helix: 2.09 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.17 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.002 0.001 HIS C 45 PHE 0.008 0.001 PHE C 16 TYR 0.011 0.001 TYR B 228 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9457 (mmp) cc_final: 0.9197 (mmt) REVERT: B 64 MET cc_start: 0.9398 (mmp) cc_final: 0.9007 (mmp) REVERT: C 64 MET cc_start: 0.9402 (mmp) cc_final: 0.9133 (mmt) REVERT: C 253 GLU cc_start: 0.9684 (pm20) cc_final: 0.9436 (pm20) outliers start: 2 outliers final: 2 residues processed: 14 average time/residue: 0.1402 time to fit residues: 2.9870 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3411 Z= 0.280 Angle : 0.623 8.662 4662 Z= 0.334 Chirality : 0.040 0.244 525 Planarity : 0.005 0.042 585 Dihedral : 4.668 23.229 447 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 12.84 % Favored : 86.34 % 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: 2.68 (0.44), residues: 402 helix: 2.07 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.08 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 69 HIS 0.003 0.001 HIS C 45 PHE 0.009 0.002 PHE C 237 TYR 0.013 0.002 TYR A 272 ARG 0.004 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9458 (mmp) cc_final: 0.9185 (mmt) REVERT: B 64 MET cc_start: 0.9416 (mmp) cc_final: 0.9024 (mmt) REVERT: C 64 MET cc_start: 0.9397 (mmp) cc_final: 0.9090 (mmm) outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.1364 time to fit residues: 2.7297 Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3411 Z= 0.228 Angle : 0.583 8.235 4662 Z= 0.312 Chirality : 0.039 0.227 525 Planarity : 0.005 0.042 585 Dihedral : 4.611 23.447 447 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.82 % Allowed : 13.66 % Favored : 85.52 % 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: 2.76 (0.44), residues: 402 helix: 2.13 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.10 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.004 0.001 HIS C 45 PHE 0.008 0.001 PHE C 16 TYR 0.010 0.001 TYR B 228 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9476 (mmp) cc_final: 0.9208 (mmt) REVERT: B 64 MET cc_start: 0.9429 (mmp) cc_final: 0.9021 (mmp) REVERT: C 64 MET cc_start: 0.9425 (mmp) cc_final: 0.9166 (mmt) outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.1399 time to fit residues: 2.8197 Evaluate side-chains 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 10 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 40.0000 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3411 Z= 0.210 Angle : 0.580 8.096 4662 Z= 0.309 Chirality : 0.038 0.228 525 Planarity : 0.004 0.041 585 Dihedral : 4.547 22.875 447 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.82 % Allowed : 13.39 % Favored : 85.79 % 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: 2.84 (0.44), residues: 402 helix: 2.18 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.18 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.003 0.001 HIS C 45 PHE 0.007 0.001 PHE C 237 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9472 (mmp) cc_final: 0.9201 (mmt) REVERT: B 64 MET cc_start: 0.9432 (mmp) cc_final: 0.8995 (mmt) REVERT: C 64 MET cc_start: 0.9394 (mmp) cc_final: 0.9129 (mmt) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.1312 time to fit residues: 2.4817 Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.0470 chunk 31 optimal weight: 7.9990 overall best weight: 2.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3411 Z= 0.145 Angle : 0.562 8.496 4662 Z= 0.295 Chirality : 0.038 0.208 525 Planarity : 0.004 0.043 585 Dihedral : 4.355 21.720 447 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 13.39 % Favored : 86.07 % 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: 2.89 (0.44), residues: 402 helix: 2.19 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.31 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 265 HIS 0.003 0.001 HIS A 244 PHE 0.008 0.001 PHE C 16 TYR 0.009 0.001 TYR B 228 ARG 0.002 0.000 ARG A 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9469 (mmp) cc_final: 0.9209 (mmt) REVERT: B 64 MET cc_start: 0.9432 (mmp) cc_final: 0.9004 (mmt) REVERT: C 64 MET cc_start: 0.9385 (mmp) cc_final: 0.9122 (mmt) REVERT: C 253 GLU cc_start: 0.9685 (pm20) cc_final: 0.9453 (pm20) outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.1442 time to fit residues: 2.8615 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.030138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.027106 restraints weight = 56090.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.027653 restraints weight = 34899.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.028039 restraints weight = 24447.852| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3411 Z= 0.148 Angle : 0.557 8.123 4662 Z= 0.294 Chirality : 0.037 0.197 525 Planarity : 0.004 0.038 585 Dihedral : 4.185 20.286 447 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.82 % Allowed : 13.11 % Favored : 86.07 % 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: 2.94 (0.43), residues: 402 helix: 2.17 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.50 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 265 HIS 0.002 0.000 HIS A 244 PHE 0.007 0.001 PHE C 250 TYR 0.009 0.001 TYR B 228 ARG 0.002 0.000 ARG A 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 856.62 seconds wall clock time: 16 minutes 8.69 seconds (968.69 seconds total)