Starting phenix.real_space_refine on Mon Sep 23 15:11:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/09_2024/7ymn_33934.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/09_2024/7ymn_33934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/09_2024/7ymn_33934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/09_2024/7ymn_33934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/09_2024/7ymn_33934.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/09_2024/7ymn_33934.cif" } resolution = 3.46 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= 0.003 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 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.09, per 1000 atoms: 0.60 Number of scatterers: 3468 At special positions: 0 Unit cell: (77.19, 150.23, 34.86, 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 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 420.0 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.744A pdb=" N GLN F 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.882A pdb=" N ILE F 328 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU F 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE D 328 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN F 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 343 through 344 removed outlier: 6.384A pdb=" N LYS F 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.558A pdb=" N ASP F 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.754A pdb=" N GLN E 307 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.901A pdb=" N ILE E 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU E 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN E 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 344 removed outlier: 6.391A pdb=" N LYS E 343 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.565A pdb=" N ASP E 358 " --> pdb=" O ASN A 359 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.67 Time building geometry restraints manager: 0.90 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: 1146 1.34 - 1.45: 369 1.45 - 1.56: 2001 1.56 - 1.68: 0 1.68 - 1.79: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" C GLY C 335 " pdb=" O GLY C 335 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" C GLY F 335 " pdb=" O GLY F 335 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" C GLY B 335 " pdb=" O GLY B 335 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.02e-02 9.61e+03 1.11e+00 bond pdb=" C GLY D 335 " pdb=" O GLY D 335 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.02e-02 9.61e+03 1.08e+00 bond pdb=" C GLY A 335 " pdb=" O GLY A 335 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.02e-02 9.61e+03 1.05e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 3876 0.85 - 1.69: 701 1.69 - 2.53: 96 2.53 - 3.38: 13 3.38 - 4.22: 24 Bond angle restraints: 4710 Sorted by residual: angle pdb=" C LEU F 357 " pdb=" N ASP F 358 " pdb=" CA ASP F 358 " ideal model delta sigma weight residual 122.10 118.12 3.98 1.66e+00 3.63e-01 5.74e+00 angle pdb=" C LEU B 357 " pdb=" N ASP B 358 " pdb=" CA ASP B 358 " ideal model delta sigma weight residual 122.10 118.14 3.96 1.66e+00 3.63e-01 5.68e+00 angle pdb=" C LEU E 357 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " ideal model delta sigma weight residual 122.10 118.14 3.96 1.66e+00 3.63e-01 5.68e+00 angle pdb=" C LEU D 357 " pdb=" N ASP D 358 " pdb=" CA ASP D 358 " ideal model delta sigma weight residual 122.10 118.15 3.95 1.66e+00 3.63e-01 5.67e+00 angle pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 122.10 118.15 3.95 1.66e+00 3.63e-01 5.67e+00 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.42: 1854 12.42 - 24.84: 216 24.84 - 37.27: 60 37.27 - 49.69: 6 49.69 - 62.11: 6 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CB GLU C 342 " pdb=" CG GLU C 342 " pdb=" CD GLU C 342 " pdb=" OE1 GLU C 342 " ideal model delta sinusoidal sigma weight residual 0.00 -62.11 62.11 1 3.00e+01 1.11e-03 5.68e+00 dihedral pdb=" CB GLU B 342 " pdb=" CG GLU B 342 " pdb=" CD GLU B 342 " pdb=" OE1 GLU B 342 " ideal model delta sinusoidal sigma weight residual 0.00 -62.11 62.11 1 3.00e+01 1.11e-03 5.68e+00 dihedral pdb=" CB GLU A 342 " pdb=" CG GLU A 342 " pdb=" CD GLU A 342 " pdb=" OE1 GLU A 342 " ideal model delta sinusoidal sigma weight residual 0.00 -62.10 62.10 1 3.00e+01 1.11e-03 5.68e+00 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 239 0.024 - 0.048: 126 0.048 - 0.072: 67 0.072 - 0.096: 40 0.096 - 0.120: 56 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA VAL B 318 " pdb=" N VAL B 318 " pdb=" C VAL B 318 " pdb=" CB VAL B 318 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA VAL F 318 " pdb=" N VAL F 318 " pdb=" C VAL F 318 " pdb=" CB VAL F 318 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL D 318 " pdb=" N VAL D 318 " pdb=" C VAL D 318 " pdb=" CB VAL D 318 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 311 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 312 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 311 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO B 312 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 312 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 312 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 311 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 312 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " 0.017 5.00e-02 4.00e+02 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 633 2.77 - 3.30: 3111 3.30 - 3.83: 5134 3.83 - 4.37: 5614 4.37 - 4.90: 12118 Nonbonded interactions: 26610 Sorted by model distance: nonbonded pdb=" NZ LYS B 370 " pdb=" OE2 GLU B 372 " model vdw 2.234 3.120 nonbonded pdb=" NZ LYS C 370 " pdb=" OE2 GLU C 372 " model vdw 2.234 3.120 nonbonded pdb=" NZ LYS E 370 " pdb=" OE2 GLU E 372 " model vdw 2.235 3.120 nonbonded pdb=" NZ LYS D 370 " pdb=" OE2 GLU D 372 " model vdw 2.235 3.120 nonbonded pdb=" NZ LYS F 370 " pdb=" OE2 GLU F 372 " model vdw 2.235 3.120 ... (remaining 26605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.190 Find NCS groups from input model: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 3522 Z= 0.486 Angle : 0.728 4.224 4710 Z= 0.414 Chirality : 0.052 0.120 528 Planarity : 0.004 0.031 600 Dihedral : 12.251 62.111 1350 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.57 % Favored : 82.43 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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 (0.25), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.009 0.003 PHE E 378 TYR 0.004 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.8094 (t0) cc_final: 0.7412 (t0) REVERT: F 349 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7385 (mmm-85) REVERT: D 345 ASP cc_start: 0.7883 (t0) cc_final: 0.7235 (t0) REVERT: E 311 LYS cc_start: 0.7417 (ttpt) cc_final: 0.6840 (tmtt) REVERT: E 345 ASP cc_start: 0.8121 (t0) cc_final: 0.7619 (t0) REVERT: E 349 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7280 (mtt90) REVERT: E 358 ASP cc_start: 0.8097 (p0) cc_final: 0.7853 (p0) REVERT: A 311 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7433 (tmtt) REVERT: A 345 ASP cc_start: 0.8414 (t0) cc_final: 0.7832 (t0) REVERT: A 349 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7460 (mmm-85) REVERT: B 345 ASP cc_start: 0.8063 (t0) cc_final: 0.7521 (t0) REVERT: B 347 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7959 (mmmm) REVERT: B 349 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7520 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3393 time to fit residues: 19.8234 Evaluate side-chains 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 359 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN B 359 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3522 Z= 0.235 Angle : 0.599 4.201 4710 Z= 0.316 Chirality : 0.049 0.123 528 Planarity : 0.004 0.037 600 Dihedral : 5.028 11.851 468 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.51 % Allowed : 7.32 % Favored : 92.17 % 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: -4.97 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.015 0.002 PHE F 378 TYR 0.006 0.001 TYR D 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: F 349 ARG cc_start: 0.7440 (mtt-85) cc_final: 0.7154 (mmm-85) REVERT: C 345 ASP cc_start: 0.8358 (t0) cc_final: 0.8053 (t0) REVERT: C 349 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7077 (mmm-85) REVERT: D 345 ASP cc_start: 0.7947 (t0) cc_final: 0.7351 (t0) REVERT: E 345 ASP cc_start: 0.8105 (t0) cc_final: 0.7556 (t0) REVERT: E 349 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7173 (mtt90) REVERT: E 358 ASP cc_start: 0.8060 (p0) cc_final: 0.7813 (p0) REVERT: A 311 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7410 (tmtt) REVERT: A 345 ASP cc_start: 0.8421 (t0) cc_final: 0.8133 (t0) REVERT: A 349 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7421 (mmm-85) REVERT: B 345 ASP cc_start: 0.7992 (t0) cc_final: 0.7301 (t0) REVERT: B 347 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7822 (mmmm) REVERT: B 349 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7482 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.3637 time to fit residues: 18.3001 Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 0.0270 overall best weight: 2.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3522 Z= 0.173 Angle : 0.542 3.940 4710 Z= 0.284 Chirality : 0.048 0.124 528 Planarity : 0.004 0.039 600 Dihedral : 4.617 11.996 468 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.25 % Allowed : 8.33 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.011 0.001 PHE F 378 TYR 0.006 0.001 TYR D 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.401 Fit side-chains REVERT: F 349 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.7082 (mmm-85) REVERT: C 345 ASP cc_start: 0.8339 (t0) cc_final: 0.7986 (t0) REVERT: C 349 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7084 (mmm-85) REVERT: D 311 LYS cc_start: 0.7433 (ttpt) cc_final: 0.6385 (tppt) REVERT: D 345 ASP cc_start: 0.7921 (t0) cc_final: 0.7402 (t0) REVERT: E 345 ASP cc_start: 0.8135 (t0) cc_final: 0.7493 (t0) REVERT: E 349 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.7090 (mtt90) REVERT: A 345 ASP cc_start: 0.8425 (t0) cc_final: 0.8078 (t0) REVERT: A 349 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7511 (mmm-85) REVERT: B 345 ASP cc_start: 0.7917 (t0) cc_final: 0.7598 (t0) REVERT: B 349 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7522 (mmm-85) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.3446 time to fit residues: 14.4566 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 3522 Z= 0.320 Angle : 0.601 4.195 4710 Z= 0.321 Chirality : 0.050 0.123 528 Planarity : 0.005 0.045 600 Dihedral : 4.953 12.313 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.76 % Allowed : 9.85 % Favored : 89.39 % 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: -4.77 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.010 0.002 PHE F 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.368 Fit side-chains REVERT: F 345 ASP cc_start: 0.7931 (t0) cc_final: 0.7459 (t0) REVERT: F 349 ARG cc_start: 0.7406 (mtt-85) cc_final: 0.7149 (mtt90) REVERT: C 345 ASP cc_start: 0.8351 (t0) cc_final: 0.8011 (t0) REVERT: C 349 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7062 (mmm-85) REVERT: D 345 ASP cc_start: 0.7943 (t0) cc_final: 0.7318 (t0) REVERT: E 345 ASP cc_start: 0.8104 (t0) cc_final: 0.7536 (t0) REVERT: E 349 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7189 (mtt90) REVERT: A 345 ASP cc_start: 0.8415 (t0) cc_final: 0.8140 (t0) REVERT: A 349 ARG cc_start: 0.7739 (mtt-85) cc_final: 0.7422 (mmm-85) REVERT: B 345 ASP cc_start: 0.7972 (t0) cc_final: 0.7318 (t0) REVERT: B 347 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7904 (mmmm) REVERT: B 349 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7539 (mmm-85) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.3340 time to fit residues: 15.1634 Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.0070 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3522 Z= 0.210 Angle : 0.545 4.002 4710 Z= 0.288 Chirality : 0.049 0.127 528 Planarity : 0.005 0.042 600 Dihedral : 4.713 12.274 468 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.25 % Allowed : 10.86 % Favored : 88.89 % 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: -4.63 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.002 TYR D 310 ARG 0.000 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.429 Fit side-chains REVERT: F 349 ARG cc_start: 0.7390 (mtt-85) cc_final: 0.7130 (mtt90) REVERT: C 345 ASP cc_start: 0.8360 (t0) cc_final: 0.8022 (t0) REVERT: C 349 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7041 (mmm-85) REVERT: D 311 LYS cc_start: 0.7438 (ttpt) cc_final: 0.6541 (tppt) REVERT: D 345 ASP cc_start: 0.7886 (t0) cc_final: 0.7294 (t0) REVERT: E 345 ASP cc_start: 0.8033 (t0) cc_final: 0.7475 (t0) REVERT: E 349 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.7131 (mtt90) REVERT: A 345 ASP cc_start: 0.8380 (t0) cc_final: 0.8087 (t0) REVERT: A 349 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7408 (mmm-85) REVERT: B 345 ASP cc_start: 0.7909 (t0) cc_final: 0.7254 (t0) REVERT: B 349 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7544 (mmm-85) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.3587 time to fit residues: 15.7889 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3522 Z= 0.343 Angle : 0.614 4.277 4710 Z= 0.329 Chirality : 0.050 0.123 528 Planarity : 0.005 0.048 600 Dihedral : 5.064 12.727 468 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.76 % Allowed : 12.63 % Favored : 86.62 % 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: -4.71 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.017 0.002 PHE F 378 TYR 0.009 0.002 TYR B 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.7952 (t0) cc_final: 0.7555 (t0) REVERT: F 349 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.7160 (mtt90) REVERT: C 345 ASP cc_start: 0.8357 (t0) cc_final: 0.8022 (t0) REVERT: C 349 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7114 (mmm-85) REVERT: D 311 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6418 (tppt) REVERT: D 345 ASP cc_start: 0.7945 (t0) cc_final: 0.7271 (t0) REVERT: E 345 ASP cc_start: 0.8049 (t0) cc_final: 0.7501 (t0) REVERT: E 349 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7204 (mtt90) REVERT: A 345 ASP cc_start: 0.8398 (t0) cc_final: 0.8140 (t0) REVERT: A 349 ARG cc_start: 0.7767 (mtt-85) cc_final: 0.7457 (mmm-85) REVERT: B 345 ASP cc_start: 0.7989 (t0) cc_final: 0.7358 (t0) REVERT: B 349 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7615 (mmm-85) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.3374 time to fit residues: 15.2637 Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 0.0030 chunk 7 optimal weight: 0.0270 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.0054 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3522 Z= 0.226 Angle : 0.562 4.081 4710 Z= 0.298 Chirality : 0.049 0.127 528 Planarity : 0.005 0.047 600 Dihedral : 4.816 12.583 468 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % 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: -4.61 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.005 0.001 PHE C 378 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: F 311 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6639 (tmtt) REVERT: F 321 LYS cc_start: 0.7157 (mttt) cc_final: 0.6428 (ttpt) REVERT: F 340 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7292 (mtpt) REVERT: F 345 ASP cc_start: 0.7959 (t0) cc_final: 0.7492 (t0) REVERT: F 349 ARG cc_start: 0.7405 (mtt-85) cc_final: 0.7163 (mtt90) REVERT: C 345 ASP cc_start: 0.8392 (t0) cc_final: 0.8054 (t0) REVERT: C 349 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7084 (mmm-85) REVERT: D 311 LYS cc_start: 0.7525 (ttpt) cc_final: 0.6405 (tppt) REVERT: D 345 ASP cc_start: 0.7918 (t0) cc_final: 0.7289 (t0) REVERT: D 372 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7370 (mp0) REVERT: E 311 LYS cc_start: 0.7281 (ttpt) cc_final: 0.6753 (tmtt) REVERT: E 345 ASP cc_start: 0.8009 (t0) cc_final: 0.7467 (t0) REVERT: E 349 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7158 (mtt90) REVERT: A 345 ASP cc_start: 0.8386 (t0) cc_final: 0.8105 (t0) REVERT: A 349 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7423 (mmm-85) REVERT: B 345 ASP cc_start: 0.7915 (t0) cc_final: 0.7274 (t0) REVERT: B 349 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7566 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3914 time to fit residues: 20.0386 Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 3522 Z= 0.316 Angle : 0.604 4.280 4710 Z= 0.323 Chirality : 0.050 0.124 528 Planarity : 0.005 0.048 600 Dihedral : 5.012 12.784 468 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.25 % Allowed : 14.14 % Favored : 85.61 % 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: -4.64 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.018 0.002 PHE F 378 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: F 311 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6656 (tmtt) REVERT: F 321 LYS cc_start: 0.7192 (mttt) cc_final: 0.6404 (ttpt) REVERT: F 340 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7375 (mtpp) REVERT: F 345 ASP cc_start: 0.8000 (t0) cc_final: 0.7550 (t0) REVERT: F 349 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7170 (mtt90) REVERT: C 345 ASP cc_start: 0.8360 (t0) cc_final: 0.8025 (t0) REVERT: C 349 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7111 (mmm-85) REVERT: D 311 LYS cc_start: 0.7533 (ttpt) cc_final: 0.6486 (tptt) REVERT: D 345 ASP cc_start: 0.7976 (t0) cc_final: 0.7308 (t0) REVERT: D 372 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7393 (mp0) REVERT: E 345 ASP cc_start: 0.8035 (t0) cc_final: 0.7279 (t0) REVERT: E 349 ARG cc_start: 0.7581 (mtt-85) cc_final: 0.7205 (mtt90) REVERT: A 345 ASP cc_start: 0.8396 (t0) cc_final: 0.8108 (t0) REVERT: A 349 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7439 (mmm-85) REVERT: B 345 ASP cc_start: 0.7975 (t0) cc_final: 0.7357 (t0) REVERT: B 349 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7616 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.3408 time to fit residues: 18.3190 Evaluate side-chains 49 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3522 Z= 0.136 Angle : 0.520 3.935 4710 Z= 0.274 Chirality : 0.048 0.129 528 Planarity : 0.005 0.048 600 Dihedral : 4.462 12.308 468 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % 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: -4.47 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.018 0.001 PHE F 378 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.378 Fit side-chains REVERT: F 349 ARG cc_start: 0.7340 (mtt-85) cc_final: 0.7097 (mtt90) REVERT: C 345 ASP cc_start: 0.8374 (t0) cc_final: 0.8039 (t0) REVERT: C 349 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7004 (mmm-85) REVERT: D 311 LYS cc_start: 0.7680 (ttpt) cc_final: 0.6575 (tppt) REVERT: D 345 ASP cc_start: 0.7826 (t0) cc_final: 0.7270 (t0) REVERT: D 372 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7354 (mp0) REVERT: E 311 LYS cc_start: 0.7393 (ttpt) cc_final: 0.6892 (tmtt) REVERT: E 345 ASP cc_start: 0.8014 (t0) cc_final: 0.7450 (t0) REVERT: E 349 ARG cc_start: 0.7527 (mtt-85) cc_final: 0.7085 (mtt90) REVERT: E 372 GLU cc_start: 0.7861 (mt-10) cc_final: 0.6891 (mp0) REVERT: A 345 ASP cc_start: 0.8414 (t0) cc_final: 0.8112 (t0) REVERT: B 311 LYS cc_start: 0.7649 (ttpt) cc_final: 0.6546 (tppt) REVERT: B 345 ASP cc_start: 0.7836 (t0) cc_final: 0.7185 (t0) REVERT: B 349 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7526 (mmm-85) REVERT: B 372 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7398 (mp0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.3442 time to fit residues: 14.7552 Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.7701 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3522 Z= 0.274 Angle : 0.577 4.054 4710 Z= 0.308 Chirality : 0.050 0.124 528 Planarity : 0.005 0.049 600 Dihedral : 4.769 12.405 468 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % 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: -4.53 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.018 0.002 PHE F 378 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.429 Fit side-chains REVERT: F 345 ASP cc_start: 0.7925 (t0) cc_final: 0.7617 (t0) REVERT: F 349 ARG cc_start: 0.7443 (mtt-85) cc_final: 0.7197 (mtt90) REVERT: C 345 ASP cc_start: 0.8362 (t0) cc_final: 0.8020 (t0) REVERT: C 349 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7078 (mmm-85) REVERT: D 345 ASP cc_start: 0.7956 (t0) cc_final: 0.7335 (t0) REVERT: D 372 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7400 (mp0) REVERT: E 311 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6782 (tmtt) REVERT: E 345 ASP cc_start: 0.8046 (t0) cc_final: 0.7493 (t0) REVERT: A 345 ASP cc_start: 0.8395 (t0) cc_final: 0.8107 (t0) REVERT: B 311 LYS cc_start: 0.7553 (ttpt) cc_final: 0.6422 (tppt) REVERT: B 345 ASP cc_start: 0.7959 (t0) cc_final: 0.7329 (t0) REVERT: B 349 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7576 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3346 time to fit residues: 15.6546 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 362 HIS ** 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 = 0.4728 r_free = 0.4728 target = 0.260029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.202797 restraints weight = 3763.565| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 0.97 r_work: 0.3789 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.3469 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3522 Z= 0.160 Angle : 0.527 4.090 4710 Z= 0.279 Chirality : 0.048 0.125 528 Planarity : 0.005 0.049 600 Dihedral : 4.488 12.440 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % 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: -4.43 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 362 PHE 0.018 0.002 PHE F 378 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.87 seconds wall clock time: 23 minutes 36.54 seconds (1416.54 seconds total)