Starting phenix.real_space_refine on Wed Mar 5 20:12:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymn_33934/03_2025/7ymn_33934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymn_33934/03_2025/7ymn_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/cci-nas-00/data/ceres_data/7ymn_33934/03_2025/7ymn_33934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymn_33934/03_2025/7ymn_33934.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymn_33934/03_2025/7ymn_33934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymn_33934/03_2025/7ymn_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-5624/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: 2.03, per 1000 atoms: 0.59 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: 0.85 Conformation dependent library (CDL) restraints added in 409.5 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: 0.35 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: 0.64 Time building geometry restraints manager: 0.95 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.040 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: 11.940 Find NCS groups from input model: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- 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 to be fit. 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: 0.3381 time to fit residues: 19.6498 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.119836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.093826 restraints weight = 4489.483| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.56 r_work: 0.3611 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1078 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= 0.219 Angle : 0.592 4.129 4710 Z= 0.312 Chirality : 0.049 0.124 528 Planarity : 0.004 0.037 600 Dihedral : 4.977 11.887 468 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -4.96 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (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 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: F 349 ARG cc_start: 0.7366 (mtt-85) cc_final: 0.7087 (mmm-85) REVERT: C 345 ASP cc_start: 0.8430 (t0) cc_final: 0.8138 (t0) REVERT: C 349 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7086 (mmm-85) REVERT: D 345 ASP cc_start: 0.7960 (t0) cc_final: 0.7415 (t0) REVERT: E 345 ASP cc_start: 0.8095 (t0) cc_final: 0.7562 (t0) REVERT: E 349 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.7145 (mtt90) REVERT: E 358 ASP cc_start: 0.7986 (p0) cc_final: 0.7696 (p0) REVERT: A 311 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7347 (tmtt) REVERT: A 345 ASP cc_start: 0.8464 (t0) cc_final: 0.8170 (t0) REVERT: A 349 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7421 (mmm-85) REVERT: B 345 ASP cc_start: 0.7994 (t0) cc_final: 0.7321 (t0) REVERT: B 347 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7850 (mmmm) REVERT: B 349 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7488 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.3480 time to fit residues: 17.1036 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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** F 368 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.252369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.198324 restraints weight = 3808.236| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 0.98 r_work: 0.3743 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.3422 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 3522 Z= 0.245 Angle : 0.579 4.109 4710 Z= 0.306 Chirality : 0.049 0.122 528 Planarity : 0.004 0.043 600 Dihedral : 4.867 12.426 468 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.51 % Allowed : 8.08 % 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: -4.85 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.011 0.002 PHE F 378 TYR 0.008 0.002 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 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.358 Fit side-chains REVERT: F 349 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7318 (mtt90) REVERT: C 345 ASP cc_start: 0.8489 (t0) cc_final: 0.8184 (t0) REVERT: C 349 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7220 (mmm-85) REVERT: D 345 ASP cc_start: 0.8094 (t0) cc_final: 0.7557 (t0) REVERT: E 345 ASP cc_start: 0.8272 (t0) cc_final: 0.7757 (t0) REVERT: E 349 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7370 (mtt90) REVERT: A 311 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7431 (tmtt) REVERT: A 345 ASP cc_start: 0.8487 (t0) cc_final: 0.8193 (t0) REVERT: A 349 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7574 (mmm-85) REVERT: B 345 ASP cc_start: 0.8093 (t0) cc_final: 0.7803 (t0) REVERT: B 347 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7947 (mmmm) REVERT: B 349 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7657 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.3187 time to fit residues: 13.7035 Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.251386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.196630 restraints weight = 3851.061| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.02 r_work: 0.3724 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work: 0.3396 rms_B_bonded: 4.77 restraints_weight: 0.1250 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1379 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= 0.271 Angle : 0.582 4.190 4710 Z= 0.309 Chirality : 0.049 0.123 528 Planarity : 0.005 0.045 600 Dihedral : 4.927 12.395 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.76 % Allowed : 9.60 % Favored : 89.65 % 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 D 349 *********************** 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 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.336 Fit side-chains REVERT: F 345 ASP cc_start: 0.8060 (t0) cc_final: 0.7659 (t0) REVERT: F 349 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.7309 (mtt90) REVERT: C 345 ASP cc_start: 0.8474 (t0) cc_final: 0.8149 (t0) REVERT: C 349 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7179 (mmm-85) REVERT: D 311 LYS cc_start: 0.7475 (ttpt) cc_final: 0.6433 (tppt) REVERT: D 345 ASP cc_start: 0.8073 (t0) cc_final: 0.7500 (t0) REVERT: E 345 ASP cc_start: 0.8207 (t0) cc_final: 0.7668 (t0) REVERT: E 349 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7338 (mtt90) REVERT: A 311 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7463 (tmtt) REVERT: A 345 ASP cc_start: 0.8474 (t0) cc_final: 0.8206 (t0) REVERT: A 349 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7551 (mmm-85) REVERT: B 345 ASP cc_start: 0.8092 (t0) cc_final: 0.7470 (t0) REVERT: B 347 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7974 (mmmm) REVERT: B 349 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7675 (mmm-85) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.2895 time to fit residues: 13.7588 Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 21 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.6102 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.256085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.201459 restraints weight = 3843.290| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.00 r_work: 0.3771 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.3446 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3522 Z= 0.197 Angle : 0.538 3.980 4710 Z= 0.283 Chirality : 0.048 0.123 528 Planarity : 0.004 0.041 600 Dihedral : 4.663 12.297 468 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.25 % Allowed : 11.11 % Favored : 88.64 % 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: -4.66 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.002 TYR D 310 ARG 0.001 0.000 ARG D 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 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.403 Fit side-chains REVERT: F 349 ARG cc_start: 0.7554 (mtt-85) cc_final: 0.7322 (mtt90) REVERT: C 345 ASP cc_start: 0.8468 (t0) cc_final: 0.8152 (t0) REVERT: C 349 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7184 (mmm-85) REVERT: D 311 LYS cc_start: 0.7547 (ttpt) cc_final: 0.6646 (tppt) REVERT: D 345 ASP cc_start: 0.8045 (t0) cc_final: 0.7520 (t0) REVERT: E 311 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6912 (tmtt) REVERT: E 345 ASP cc_start: 0.8246 (t0) cc_final: 0.7732 (t0) REVERT: E 349 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.7307 (mtt90) REVERT: A 311 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7451 (tmtt) REVERT: A 345 ASP cc_start: 0.8470 (t0) cc_final: 0.8192 (t0) REVERT: B 311 LYS cc_start: 0.7855 (ttpt) cc_final: 0.6734 (tppt) REVERT: B 345 ASP cc_start: 0.8073 (t0) cc_final: 0.7796 (t0) REVERT: B 347 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7954 (mmmm) REVERT: B 349 ARG cc_start: 0.8011 (mtt-85) cc_final: 0.7710 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.3757 time to fit residues: 17.1723 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4698 r_free = 0.4698 target = 0.254916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.199010 restraints weight = 3851.742| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 0.99 r_work: 0.3744 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.3425 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 3522 Z= 0.249 Angle : 0.562 4.015 4710 Z= 0.298 Chirality : 0.049 0.122 528 Planarity : 0.004 0.040 600 Dihedral : 4.760 12.307 468 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.51 % Allowed : 12.37 % Favored : 87.12 % 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: -4.67 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.006 0.002 PHE C 378 TYR 0.008 0.002 TYR B 310 ARG 0.001 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 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.356 Fit side-chains REVERT: F 345 ASP cc_start: 0.8062 (t0) cc_final: 0.7713 (t0) REVERT: F 349 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.7315 (mtt90) REVERT: C 345 ASP cc_start: 0.8520 (t0) cc_final: 0.8201 (t0) REVERT: C 349 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7226 (mmm-85) REVERT: D 311 LYS cc_start: 0.7604 (ttpt) cc_final: 0.6574 (tppt) REVERT: D 345 ASP cc_start: 0.8019 (t0) cc_final: 0.7448 (t0) REVERT: E 311 LYS cc_start: 0.7377 (ttpt) cc_final: 0.6891 (tmtt) REVERT: E 345 ASP cc_start: 0.8192 (t0) cc_final: 0.7659 (t0) REVERT: A 311 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7444 (tmtt) REVERT: A 345 ASP cc_start: 0.8470 (t0) cc_final: 0.8204 (t0) REVERT: B 311 LYS cc_start: 0.7783 (ttpt) cc_final: 0.6665 (tppt) REVERT: B 345 ASP cc_start: 0.8053 (t0) cc_final: 0.7428 (t0) REVERT: B 347 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7991 (mmmm) REVERT: B 349 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7695 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.3350 time to fit residues: 16.1356 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.115526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.088604 restraints weight = 4642.078| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.60 r_work: 0.3535 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1595 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= 0.340 Angle : 0.614 4.488 4710 Z= 0.329 Chirality : 0.051 0.123 528 Planarity : 0.005 0.046 600 Dihedral : 5.083 12.657 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.01 % Allowed : 12.88 % 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: -4.69 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.23), 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 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 *********************** 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 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: F 321 LYS cc_start: 0.7124 (mttt) cc_final: 0.6437 (ttpt) REVERT: F 345 ASP cc_start: 0.8026 (t0) cc_final: 0.7641 (t0) REVERT: F 349 ARG cc_start: 0.7419 (mtt-85) cc_final: 0.7196 (mtt90) REVERT: C 345 ASP cc_start: 0.8426 (t0) cc_final: 0.8132 (t0) REVERT: C 349 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7172 (mmm-85) REVERT: D 311 LYS cc_start: 0.7520 (ttpt) cc_final: 0.6549 (tptt) REVERT: D 345 ASP cc_start: 0.8026 (t0) cc_final: 0.7389 (t0) REVERT: D 372 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7559 (mp0) REVERT: E 311 LYS cc_start: 0.7274 (ttpt) cc_final: 0.6696 (tmtt) REVERT: E 345 ASP cc_start: 0.8093 (t0) cc_final: 0.7359 (t0) REVERT: A 311 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7395 (tmtt) REVERT: A 345 ASP cc_start: 0.8437 (t0) cc_final: 0.8147 (t0) REVERT: B 345 ASP cc_start: 0.8050 (t0) cc_final: 0.7470 (t0) REVERT: B 349 ARG cc_start: 0.7950 (mtt-85) cc_final: 0.7517 (mmm-85) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.3231 time to fit residues: 17.2173 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.114826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.087188 restraints weight = 4580.818| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.62 r_work: 0.3564 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1727 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= 0.277 Angle : 0.598 4.635 4710 Z= 0.320 Chirality : 0.050 0.123 528 Planarity : 0.005 0.047 600 Dihedral : 4.968 12.635 468 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.76 % Allowed : 14.14 % Favored : 85.10 % 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: -4.60 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.018 0.002 PHE E 378 TYR 0.009 0.002 TYR D 310 ARG 0.003 0.000 ARG E 349 *********************** 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 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: F 321 LYS cc_start: 0.7106 (mttt) cc_final: 0.6353 (ttpt) REVERT: F 343 LYS cc_start: 0.6644 (mttt) cc_final: 0.6134 (mptt) REVERT: F 345 ASP cc_start: 0.8013 (t0) cc_final: 0.7617 (t0) REVERT: F 349 ARG cc_start: 0.7379 (mtt-85) cc_final: 0.7173 (mtt90) REVERT: C 322 CYS cc_start: 0.8525 (t) cc_final: 0.8217 (m) REVERT: C 345 ASP cc_start: 0.8425 (t0) cc_final: 0.8112 (t0) REVERT: C 349 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7156 (mmm-85) REVERT: D 311 LYS cc_start: 0.7515 (ttpt) cc_final: 0.6503 (tppt) REVERT: D 345 ASP cc_start: 0.8046 (t0) cc_final: 0.7402 (t0) REVERT: D 372 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7558 (mp0) REVERT: E 311 LYS cc_start: 0.7267 (ttpt) cc_final: 0.6703 (tmtt) REVERT: E 345 ASP cc_start: 0.8052 (t0) cc_final: 0.7338 (t0) REVERT: A 311 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7444 (tmtt) REVERT: A 322 CYS cc_start: 0.8520 (t) cc_final: 0.8146 (m) REVERT: A 345 ASP cc_start: 0.8463 (t0) cc_final: 0.8160 (t0) REVERT: B 311 LYS cc_start: 0.7504 (ttpt) cc_final: 0.6413 (tppt) REVERT: B 345 ASP cc_start: 0.8010 (t0) cc_final: 0.7424 (t0) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.3222 time to fit residues: 19.2039 Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.113107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.085788 restraints weight = 4631.058| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.61 r_work: 0.3531 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3522 Z= 0.336 Angle : 0.627 4.773 4710 Z= 0.336 Chirality : 0.051 0.123 528 Planarity : 0.005 0.047 600 Dihedral : 5.130 12.689 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 1.01 % Allowed : 14.39 % Favored : 84.60 % 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 0.004 0.001 HIS C 362 PHE 0.019 0.003 PHE E 378 TYR 0.010 0.002 TYR B 310 ARG 0.003 0.000 ARG E 349 *********************** 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 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 321 LYS cc_start: 0.7154 (mttt) cc_final: 0.6337 (ttpt) REVERT: F 345 ASP cc_start: 0.8131 (t0) cc_final: 0.7762 (t0) REVERT: C 322 CYS cc_start: 0.8527 (t) cc_final: 0.8226 (m) REVERT: C 345 ASP cc_start: 0.8461 (t0) cc_final: 0.8152 (t0) REVERT: D 311 LYS cc_start: 0.7513 (ttpt) cc_final: 0.6566 (tptt) REVERT: D 345 ASP cc_start: 0.8122 (t0) cc_final: 0.7458 (t0) REVERT: D 372 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7554 (mp0) REVERT: E 345 ASP cc_start: 0.8108 (t0) cc_final: 0.7336 (t0) REVERT: A 311 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7486 (tmtt) REVERT: A 322 CYS cc_start: 0.8572 (t) cc_final: 0.8155 (m) REVERT: A 345 ASP cc_start: 0.8434 (t0) cc_final: 0.8139 (t0) REVERT: B 311 LYS cc_start: 0.7467 (ttpt) cc_final: 0.6460 (tppt) REVERT: B 345 ASP cc_start: 0.8057 (t0) cc_final: 0.7484 (t0) REVERT: B 349 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7691 (mmm-85) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.3163 time to fit residues: 18.5947 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.114352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.086840 restraints weight = 4640.234| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.62 r_work: 0.3559 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3522 Z= 0.288 Angle : 0.605 4.779 4710 Z= 0.324 Chirality : 0.050 0.125 528 Planarity : 0.005 0.049 600 Dihedral : 5.041 12.653 468 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.76 % Allowed : 14.65 % Favored : 84.60 % 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: -4.57 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.019 0.002 PHE E 378 TYR 0.010 0.002 TYR B 310 ARG 0.002 0.000 ARG E 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 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: F 311 LYS cc_start: 0.7112 (ttpt) cc_final: 0.6582 (tmtt) REVERT: F 343 LYS cc_start: 0.6680 (mttt) cc_final: 0.6136 (mptt) REVERT: F 345 ASP cc_start: 0.8119 (t0) cc_final: 0.7753 (t0) REVERT: C 322 CYS cc_start: 0.8494 (t) cc_final: 0.8283 (m) REVERT: C 345 ASP cc_start: 0.8463 (t0) cc_final: 0.8125 (t0) REVERT: D 345 ASP cc_start: 0.8112 (t0) cc_final: 0.7471 (t0) REVERT: D 372 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7558 (mp0) REVERT: E 311 LYS cc_start: 0.7241 (ttpt) cc_final: 0.6728 (tmtt) REVERT: E 345 ASP cc_start: 0.8101 (t0) cc_final: 0.7354 (t0) REVERT: A 311 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7462 (tmtt) REVERT: A 322 CYS cc_start: 0.8530 (t) cc_final: 0.8176 (m) REVERT: A 345 ASP cc_start: 0.8464 (t0) cc_final: 0.8157 (t0) REVERT: B 311 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6437 (tppt) REVERT: B 345 ASP cc_start: 0.8023 (t0) cc_final: 0.7482 (t0) REVERT: B 349 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7701 (mmm-85) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.3074 time to fit residues: 18.7563 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 0.0770 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.4942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.260943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.204981 restraints weight = 3761.510| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 0.98 r_work: 0.3817 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.3493 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3522 Z= 0.140 Angle : 0.527 4.376 4710 Z= 0.278 Chirality : 0.048 0.127 528 Planarity : 0.005 0.048 600 Dihedral : 4.507 12.408 468 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.25 % Allowed : 15.15 % Favored : 84.60 % 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: -4.48 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.018 0.002 PHE F 378 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.04 seconds wall clock time: 37 minutes 49.33 seconds (2269.33 seconds total)