Starting phenix.real_space_refine on Fri Aug 22 13:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymn_33934/08_2025/7ymn_33934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymn_33934/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ymn_33934/08_2025/7ymn_33934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymn_33934/08_2025/7ymn_33934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ymn_33934/08_2025/7ymn_33934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymn_33934/08_2025/7ymn_33934.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" 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, D, E, A, B Time building chain proxies: 0.47, per 1000 atoms: 0.14 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: 0.22 Conformation dependent library (CDL) restraints added in 93.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.07 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: 0.35 Time building geometry restraints manager: 0.30 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: 0.01 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' selection = chain 'B' } 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: 1.490 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.040 ------------------------------------------------------------------------------- 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= 0.343 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 349 TYR 0.004 0.002 TYR E 310 PHE 0.009 0.003 PHE E 378 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 3522) covalent geometry : angle 0.72819 ( 4710) hydrogen bonds : bond 0.27415 ( 10) hydrogen bonds : angle 9.65088 ( 30) *********************** 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 : 0.088 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: 0.7304 (mmm-85) REVERT: C 349 ARG cc_start: 0.7696 (mtt-85) cc_final: 0.7274 (mmm-85) REVERT: D 345 ASP cc_start: 0.7883 (t0) cc_final: 0.7234 (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: 0.7281 (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: 0.7521 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1477 time to fit residues: 8.5504 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 : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.112868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.086672 restraints weight = 4817.190| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.66 r_work: 0.3459 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3522 Z= 0.296 Angle : 0.720 4.688 4710 Z= 0.388 Chirality : 0.053 0.123 528 Planarity : 0.005 0.043 600 Dihedral : 5.717 12.504 468 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 0.51 % Allowed : 8.59 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.11 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.011 0.002 TYR D 310 PHE 0.016 0.003 PHE F 378 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 3522) covalent geometry : angle 0.71978 ( 4710) hydrogen bonds : bond 0.05308 ( 10) hydrogen bonds : angle 6.19965 ( 30) *********************** 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 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.097 Fit side-chains REVERT: F 345 ASP cc_start: 0.8075 (t0) cc_final: 0.7466 (t0) REVERT: C 345 ASP cc_start: 0.8448 (t0) cc_final: 0.8192 (t0) REVERT: C 349 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7392 (mmm-85) REVERT: D 345 ASP cc_start: 0.8006 (t0) cc_final: 0.7438 (t0) REVERT: E 311 LYS cc_start: 0.7371 (ttpt) cc_final: 0.6734 (tmtt) REVERT: E 345 ASP cc_start: 0.8136 (t0) cc_final: 0.7406 (t0) REVERT: E 349 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7211 (mtt90) REVERT: A 311 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7449 (tmtt) REVERT: A 345 ASP cc_start: 0.8435 (t0) cc_final: 0.7903 (t0) REVERT: A 349 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7498 (mmm-85) REVERT: B 345 ASP cc_start: 0.8136 (t0) cc_final: 0.7585 (t0) REVERT: B 349 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7593 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.1765 time to fit residues: 9.3421 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4032 r_free = 0.4032 target = 0.111085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.084151 restraints weight = 4800.305| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.64 r_work: 0.3487 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3522 Z= 0.288 Angle : 0.709 4.718 4710 Z= 0.381 Chirality : 0.052 0.124 528 Planarity : 0.006 0.049 600 Dihedral : 5.722 13.491 468 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 0.51 % Allowed : 12.12 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.97 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.011 0.002 TYR D 310 PHE 0.009 0.002 PHE C 378 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 3522) covalent geometry : angle 0.70928 ( 4710) hydrogen bonds : bond 0.04296 ( 10) hydrogen bonds : angle 5.94625 ( 30) *********************** 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 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.150 Fit side-chains REVERT: F 345 ASP cc_start: 0.8069 (t0) cc_final: 0.7437 (t0) REVERT: C 345 ASP cc_start: 0.8392 (t0) cc_final: 0.8076 (t0) REVERT: C 349 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7450 (mmm-85) REVERT: D 311 LYS cc_start: 0.7412 (ttpt) cc_final: 0.6426 (tppt) REVERT: D 345 ASP cc_start: 0.8026 (t0) cc_final: 0.7473 (t0) REVERT: E 311 LYS cc_start: 0.7507 (ttpt) cc_final: 0.6826 (tmtt) REVERT: E 345 ASP cc_start: 0.8138 (t0) cc_final: 0.7384 (t0) REVERT: E 349 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7345 (mtt90) REVERT: A 311 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7473 (tmtt) REVERT: A 345 ASP cc_start: 0.8416 (t0) cc_final: 0.8137 (t0) REVERT: A 349 ARG cc_start: 0.7771 (mtt-85) cc_final: 0.7529 (mmm-85) REVERT: B 345 ASP cc_start: 0.8123 (t0) cc_final: 0.7550 (t0) REVERT: B 349 ARG cc_start: 0.7962 (mtt-85) cc_final: 0.7586 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1703 time to fit residues: 8.3193 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 35 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4145 r_free = 0.4145 target = 0.118379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.091400 restraints weight = 4500.652| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.60 r_work: 0.3594 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1490 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= 0.138 Angle : 0.584 4.275 4710 Z= 0.306 Chirality : 0.049 0.125 528 Planarity : 0.005 0.045 600 Dihedral : 5.064 12.954 468 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.51 % Allowed : 11.87 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.79 (0.28), 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 ARG 0.001 0.000 ARG D 349 TYR 0.007 0.002 TYR D 310 PHE 0.015 0.001 PHE F 378 HIS 0.006 0.002 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3522) covalent geometry : angle 0.58362 ( 4710) hydrogen bonds : bond 0.03054 ( 10) hydrogen bonds : angle 5.97803 ( 30) *********************** 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 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.145 Fit side-chains REVERT: C 311 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7335 (tmtt) REVERT: C 345 ASP cc_start: 0.8408 (t0) cc_final: 0.8076 (t0) REVERT: C 349 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7452 (mmm-85) REVERT: D 311 LYS cc_start: 0.7419 (ttpt) cc_final: 0.6365 (tppt) REVERT: D 345 ASP cc_start: 0.7979 (t0) cc_final: 0.7502 (t0) REVERT: E 311 LYS cc_start: 0.7460 (ttpt) cc_final: 0.6823 (tmtt) REVERT: E 345 ASP cc_start: 0.8111 (t0) cc_final: 0.7533 (t0) REVERT: E 349 ARG cc_start: 0.7529 (mtt-85) cc_final: 0.7194 (mtt90) REVERT: A 311 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7412 (tmtt) REVERT: A 345 ASP cc_start: 0.8357 (t0) cc_final: 0.8044 (t0) REVERT: A 349 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7474 (mmm-85) REVERT: B 345 ASP cc_start: 0.7982 (t0) cc_final: 0.7333 (t0) REVERT: B 347 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7922 (mmmm) REVERT: B 349 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7570 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.1692 time to fit residues: 8.4774 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 0.0970 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.3984 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4098 r_free = 0.4098 target = 0.115749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.088763 restraints weight = 4645.637| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.60 r_work: 0.3543 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1489 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= 0.213 Angle : 0.626 4.381 4710 Z= 0.333 Chirality : 0.050 0.123 528 Planarity : 0.005 0.044 600 Dihedral : 5.222 12.591 468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.51 % Allowed : 13.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.81 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.009 0.002 TYR D 310 PHE 0.007 0.002 PHE C 378 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 3522) covalent geometry : angle 0.62621 ( 4710) hydrogen bonds : bond 0.03259 ( 10) hydrogen bonds : angle 5.67067 ( 30) *********************** 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 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 321 LYS cc_start: 0.7125 (mttt) cc_final: 0.6398 (ttpt) REVERT: F 345 ASP cc_start: 0.7986 (t0) cc_final: 0.7567 (t0) REVERT: C 311 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7353 (tmtt) REVERT: C 345 ASP cc_start: 0.8428 (t0) cc_final: 0.8088 (t0) REVERT: C 349 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7511 (mmm-85) REVERT: D 311 LYS cc_start: 0.7416 (ttpt) cc_final: 0.6420 (tppt) REVERT: D 345 ASP cc_start: 0.8003 (t0) cc_final: 0.7436 (t0) REVERT: E 311 LYS cc_start: 0.7452 (ttpt) cc_final: 0.6869 (tmtt) REVERT: E 345 ASP cc_start: 0.8124 (t0) cc_final: 0.7549 (t0) REVERT: A 311 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7485 (tmtt) REVERT: A 345 ASP cc_start: 0.8381 (t0) cc_final: 0.8073 (t0) REVERT: A 349 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7522 (mmm-85) REVERT: B 345 ASP cc_start: 0.8087 (t0) cc_final: 0.7490 (t0) REVERT: B 349 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7603 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1744 time to fit residues: 9.0296 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 11 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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** D 368 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.113273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.085730 restraints weight = 4663.887| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.64 r_work: 0.3537 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3522 Z= 0.223 Angle : 0.635 4.428 4710 Z= 0.340 Chirality : 0.051 0.124 528 Planarity : 0.005 0.043 600 Dihedral : 5.335 13.248 468 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.51 % Allowed : 14.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.81 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.010 0.002 TYR D 310 PHE 0.017 0.002 PHE F 378 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 3522) covalent geometry : angle 0.63526 ( 4710) hydrogen bonds : bond 0.03274 ( 10) hydrogen bonds : angle 5.57455 ( 30) *********************** 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 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: F 321 LYS cc_start: 0.7145 (mttt) cc_final: 0.6449 (ttpt) REVERT: F 345 ASP cc_start: 0.7956 (t0) cc_final: 0.7520 (t0) REVERT: C 311 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7319 (tmtt) REVERT: C 345 ASP cc_start: 0.8408 (t0) cc_final: 0.8079 (t0) REVERT: C 349 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7516 (mmm-85) REVERT: D 345 ASP cc_start: 0.7983 (t0) cc_final: 0.7373 (t0) REVERT: E 311 LYS cc_start: 0.7463 (ttpt) cc_final: 0.6860 (tmtt) REVERT: E 345 ASP cc_start: 0.8106 (t0) cc_final: 0.7367 (t0) REVERT: A 311 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7525 (tmtt) REVERT: A 322 CYS cc_start: 0.8561 (t) cc_final: 0.8195 (m) REVERT: A 345 ASP cc_start: 0.8374 (t0) cc_final: 0.8060 (t0) REVERT: A 349 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7507 (mmm-85) REVERT: B 345 ASP cc_start: 0.8079 (t0) cc_final: 0.7500 (t0) REVERT: B 349 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7552 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.1521 time to fit residues: 7.9284 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 25 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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** ** A 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 = 0.4056 r_free = 0.4056 target = 0.112577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.085059 restraints weight = 4711.891| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.63 r_work: 0.3521 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3522 Z= 0.237 Angle : 0.649 4.459 4710 Z= 0.348 Chirality : 0.051 0.124 528 Planarity : 0.005 0.048 600 Dihedral : 5.419 13.145 468 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.76 % Allowed : 15.15 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.81 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.011 0.002 TYR D 310 PHE 0.017 0.002 PHE E 378 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 3522) covalent geometry : angle 0.64874 ( 4710) hydrogen bonds : bond 0.03183 ( 10) hydrogen bonds : angle 5.50171 ( 30) *********************** 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: 3 poor density : 46 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: F 321 LYS cc_start: 0.7136 (mttt) cc_final: 0.6398 (ttpt) REVERT: F 345 ASP cc_start: 0.8025 (t0) cc_final: 0.7578 (t0) REVERT: C 311 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7361 (tmtt) REVERT: C 322 CYS cc_start: 0.8542 (t) cc_final: 0.8272 (m) REVERT: C 345 ASP cc_start: 0.8420 (t0) cc_final: 0.8090 (t0) REVERT: C 349 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7521 (mmm-85) REVERT: D 345 ASP cc_start: 0.7967 (t0) cc_final: 0.7368 (t0) REVERT: E 311 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6892 (tmtt) REVERT: E 345 ASP cc_start: 0.8136 (t0) cc_final: 0.7404 (t0) REVERT: A 311 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7566 (tmtt) REVERT: A 322 CYS cc_start: 0.8544 (t) cc_final: 0.8250 (m) REVERT: A 345 ASP cc_start: 0.8372 (t0) cc_final: 0.8064 (t0) REVERT: A 349 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7528 (mmm-85) REVERT: B 345 ASP cc_start: 0.8100 (t0) cc_final: 0.7529 (t0) REVERT: B 349 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7586 (mmm-85) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.1561 time to fit residues: 8.3678 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4037 r_free = 0.4037 target = 0.111267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083977 restraints weight = 4804.956| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.62 r_work: 0.3508 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3522 Z= 0.291 Angle : 0.705 4.654 4710 Z= 0.380 Chirality : 0.053 0.125 528 Planarity : 0.006 0.051 600 Dihedral : 5.722 13.853 468 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.64 % Favored : 85.36 % Rotamer: Outliers : 0.76 % Allowed : 14.90 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.88 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.013 0.003 TYR B 310 PHE 0.018 0.003 PHE F 378 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 3522) covalent geometry : angle 0.70459 ( 4710) hydrogen bonds : bond 0.03400 ( 10) hydrogen bonds : angle 5.51193 ( 30) *********************** 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 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.099 Fit side-chains REVERT: F 311 LYS cc_start: 0.7420 (ttpt) cc_final: 0.6828 (tmtt) REVERT: F 321 LYS cc_start: 0.7143 (mttt) cc_final: 0.6389 (ttpt) REVERT: F 345 ASP cc_start: 0.8055 (t0) cc_final: 0.7613 (t0) REVERT: C 311 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7394 (tmtt) REVERT: C 322 CYS cc_start: 0.8564 (t) cc_final: 0.8299 (m) REVERT: C 345 ASP cc_start: 0.8460 (t0) cc_final: 0.8139 (t0) REVERT: C 349 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7594 (mmm-85) REVERT: D 311 LYS cc_start: 0.7534 (ttpt) cc_final: 0.6519 (tppt) REVERT: D 345 ASP cc_start: 0.8025 (t0) cc_final: 0.7406 (t0) REVERT: E 311 LYS cc_start: 0.7499 (ttpt) cc_final: 0.6856 (tmtt) REVERT: E 345 ASP cc_start: 0.8218 (t0) cc_final: 0.7460 (t0) REVERT: A 311 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7576 (tmtt) REVERT: A 322 CYS cc_start: 0.8546 (t) cc_final: 0.8251 (m) REVERT: A 345 ASP cc_start: 0.8415 (t0) cc_final: 0.8125 (t0) REVERT: A 349 ARG cc_start: 0.7786 (mtt-85) cc_final: 0.7531 (mmm-85) REVERT: B 345 ASP cc_start: 0.8094 (t0) cc_final: 0.7536 (t0) REVERT: B 349 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7557 (mmm-85) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1353 time to fit residues: 7.5686 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D 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 41 optimal weight: 0.0050 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.0070 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 2.2018 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4194 r_free = 0.4194 target = 0.122348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.095243 restraints weight = 4386.027| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.54 r_work: 0.3650 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1978 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= 0.120 Angle : 0.573 4.523 4710 Z= 0.303 Chirality : 0.049 0.126 528 Planarity : 0.005 0.051 600 Dihedral : 4.943 11.385 468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.25 % Allowed : 15.66 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.63 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.008 0.002 TYR B 310 PHE 0.018 0.002 PHE F 378 HIS 0.007 0.002 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3522) covalent geometry : angle 0.57343 ( 4710) hydrogen bonds : bond 0.02505 ( 10) hydrogen bonds : angle 5.78648 ( 30) *********************** 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 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.144 Fit side-chains REVERT: C 311 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7371 (tmtt) REVERT: C 345 ASP cc_start: 0.8366 (t0) cc_final: 0.8026 (t0) REVERT: C 349 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.7495 (mmm-85) REVERT: D 345 ASP cc_start: 0.7870 (t0) cc_final: 0.7329 (t0) REVERT: D 372 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7361 (mp0) REVERT: E 311 LYS cc_start: 0.7440 (ttpt) cc_final: 0.6853 (tmtt) REVERT: E 345 ASP cc_start: 0.7983 (t0) cc_final: 0.7407 (t0) REVERT: A 311 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7430 (tmtt) REVERT: A 345 ASP cc_start: 0.8349 (t0) cc_final: 0.8012 (t0) REVERT: A 349 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7382 (mmm-85) REVERT: B 349 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7424 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1446 time to fit residues: 7.2870 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 : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4242 r_free = 0.4242 target = 0.124209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.096860 restraints weight = 4323.714| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.62 r_work: 0.3681 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2146 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= 0.103 Angle : 0.544 4.674 4710 Z= 0.285 Chirality : 0.048 0.125 528 Planarity : 0.005 0.050 600 Dihedral : 4.593 11.548 468 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.25 % Allowed : 16.41 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.52 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.007 0.001 TYR B 310 PHE 0.018 0.002 PHE F 378 HIS 0.006 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3522) covalent geometry : angle 0.54382 ( 4710) hydrogen bonds : bond 0.02445 ( 10) hydrogen bonds : angle 5.90113 ( 30) ********************** 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 to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.147 Fit side-chains REVERT: F 349 ARG cc_start: 0.7323 (mtt90) cc_final: 0.6772 (mmm-85) REVERT: C 311 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7413 (tmtt) REVERT: C 345 ASP cc_start: 0.8393 (t0) cc_final: 0.8041 (t0) REVERT: C 349 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7578 (mmm-85) REVERT: D 345 ASP cc_start: 0.7821 (t0) cc_final: 0.7364 (t0) REVERT: D 372 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7361 (mp0) REVERT: E 345 ASP cc_start: 0.7996 (t0) cc_final: 0.7455 (t0) REVERT: E 372 GLU cc_start: 0.7919 (mt-10) cc_final: 0.6875 (mp0) REVERT: A 349 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7389 (mmm-85) REVERT: B 345 ASP cc_start: 0.7463 (t0) cc_final: 0.7092 (t0) REVERT: B 349 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7411 (mmm-85) REVERT: B 372 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7465 (mp0) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1673 time to fit residues: 7.6270 Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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** ** A 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 = 0.4159 r_free = 0.4159 target = 0.119847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.093104 restraints weight = 4475.313| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.54 r_work: 0.3616 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3522 Z= 0.177 Angle : 0.601 4.335 4710 Z= 0.318 Chirality : 0.050 0.123 528 Planarity : 0.005 0.050 600 Dihedral : 4.901 12.328 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.25 % Allowed : 16.67 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (0.30), 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 ARG 0.001 0.000 ARG D 349 TYR 0.009 0.002 TYR B 310 PHE 0.018 0.002 PHE F 378 HIS 0.006 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3522) covalent geometry : angle 0.60070 ( 4710) hydrogen bonds : bond 0.02788 ( 10) hydrogen bonds : angle 5.60055 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.68 seconds wall clock time: 20 minutes 38.09 seconds (1238.09 seconds total)