Starting phenix.real_space_refine on Tue Feb 11 01:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymn_33934/02_2025/7ymn_33934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymn_33934/02_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_33934/02_2025/7ymn_33934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymn_33934/02_2025/7ymn_33934.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymn_33934/02_2025/7ymn_33934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymn_33934/02_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-5592/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: 2.22, per 1000 atoms: 0.64 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: 0.69 Conformation dependent library (CDL) restraints added in 415.3 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: 0.32 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: 0.72 Time building geometry restraints manager: 0.84 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: 1.270 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.050 Find NCS groups from input model: 0.080 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- 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 : 0.324 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: 0.3510 time to fit residues: 20.2611 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 359 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN B 359 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.119045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.092958 restraints weight = 4510.065| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.60 r_work: 0.3602 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3522 Z= 0.235 Angle : 0.599 4.201 4710 Z= 0.316 Chirality : 0.049 0.123 528 Planarity : 0.004 0.037 600 Dihedral : 5.028 11.851 468 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.51 % Allowed : 7.32 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.015 0.002 PHE F 378 TYR 0.006 0.001 TYR D 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: F 349 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.7097 (mmm-85) REVERT: C 345 ASP cc_start: 0.8439 (t0) cc_final: 0.8176 (t0) REVERT: C 349 ARG cc_start: 0.7663 (mtt90) cc_final: 0.7087 (mmm-85) REVERT: D 345 ASP cc_start: 0.7947 (t0) cc_final: 0.7378 (t0) REVERT: E 345 ASP cc_start: 0.8098 (t0) cc_final: 0.7555 (t0) REVERT: E 349 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.7156 (mtt90) REVERT: E 358 ASP cc_start: 0.8053 (p0) cc_final: 0.7779 (p0) REVERT: A 311 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7361 (tmtt) REVERT: A 345 ASP cc_start: 0.8471 (t0) cc_final: 0.8192 (t0) REVERT: A 349 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7428 (mmm-85) REVERT: B 345 ASP cc_start: 0.8002 (t0) cc_final: 0.7337 (t0) REVERT: B 347 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7859 (mmmm) REVERT: B 349 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7495 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.3410 time to fit residues: 17.1874 Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 0.2980 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 = 0.4680 r_free = 0.4680 target = 0.250689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.196555 restraints weight = 3827.373| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 0.99 r_work: 0.3724 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work: 0.3400 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1242 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= 0.271 Angle : 0.597 4.189 4710 Z= 0.316 Chirality : 0.049 0.123 528 Planarity : 0.004 0.042 600 Dihedral : 4.976 12.373 468 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.51 % Allowed : 8.33 % Favored : 91.16 % 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: -4.89 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.012 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 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.422 Fit side-chains REVERT: F 349 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7187 (mtt90) REVERT: C 345 ASP cc_start: 0.8461 (t0) cc_final: 0.8154 (t0) REVERT: C 349 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7115 (mmm-85) REVERT: D 311 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6389 (tppt) REVERT: D 345 ASP cc_start: 0.8017 (t0) cc_final: 0.7448 (t0) REVERT: E 345 ASP cc_start: 0.8170 (t0) cc_final: 0.7634 (t0) REVERT: E 349 ARG cc_start: 0.7568 (mtt-85) cc_final: 0.7243 (mtt90) REVERT: A 311 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7378 (tmtt) REVERT: A 345 ASP cc_start: 0.8486 (t0) cc_final: 0.8194 (t0) REVERT: A 349 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7488 (mmm-85) REVERT: A 379 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7370 (mmm160) REVERT: B 345 ASP cc_start: 0.8033 (t0) cc_final: 0.7721 (t0) REVERT: B 347 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7931 (mmmm) REVERT: B 349 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7560 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.3215 time to fit residues: 14.9391 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4064 r_free = 0.4064 target = 0.112785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.085512 restraints weight = 4711.368| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.65 r_work: 0.3524 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1318 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= 0.345 Angle : 0.630 4.415 4710 Z= 0.337 Chirality : 0.051 0.124 528 Planarity : 0.005 0.045 600 Dihedral : 5.265 12.814 468 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.76 % Allowed : 10.61 % 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: -4.86 (0.28), 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 0.008 0.002 PHE C 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.456 Fit side-chains REVERT: F 345 ASP cc_start: 0.8005 (t0) cc_final: 0.7633 (t0) REVERT: F 349 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7214 (mtt90) REVERT: C 345 ASP cc_start: 0.8462 (t0) cc_final: 0.8164 (t0) REVERT: C 349 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7109 (mmm-85) REVERT: D 345 ASP cc_start: 0.8016 (t0) cc_final: 0.7424 (t0) REVERT: E 345 ASP cc_start: 0.8099 (t0) cc_final: 0.7552 (t0) REVERT: E 349 ARG cc_start: 0.7590 (mtt-85) cc_final: 0.7268 (mtt90) REVERT: A 311 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7430 (tmtt) REVERT: A 345 ASP cc_start: 0.8470 (t0) cc_final: 0.8214 (t0) REVERT: A 349 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7516 (mmm-85) REVERT: A 379 ARG cc_start: 0.7554 (mmt180) cc_final: 0.7316 (mmm160) REVERT: B 345 ASP cc_start: 0.8071 (t0) cc_final: 0.7468 (t0) REVERT: B 347 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7966 (mmmm) REVERT: B 349 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7629 (mmm-85) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.3723 time to fit residues: 18.1799 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 : 0.424 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.115161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.087534 restraints weight = 4665.384| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.66 r_work: 0.3579 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1462 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= 0.256 Angle : 0.579 4.210 4710 Z= 0.308 Chirality : 0.049 0.124 528 Planarity : 0.005 0.045 600 Dihedral : 5.001 12.787 468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % 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: -4.76 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.016 0.002 PHE F 378 TYR 0.009 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 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.391 Fit side-chains REVERT: F 321 LYS cc_start: 0.7113 (mttt) cc_final: 0.6398 (ttpt) REVERT: F 345 ASP cc_start: 0.8041 (t0) cc_final: 0.7589 (t0) REVERT: F 349 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.7151 (mtt90) REVERT: C 345 ASP cc_start: 0.8440 (t0) cc_final: 0.8105 (t0) REVERT: C 349 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7152 (mmm-85) REVERT: D 311 LYS cc_start: 0.7415 (ttpt) cc_final: 0.6436 (tppt) REVERT: D 345 ASP cc_start: 0.8035 (t0) cc_final: 0.7468 (t0) REVERT: E 311 LYS cc_start: 0.7268 (ttpt) cc_final: 0.6736 (tmtt) REVERT: E 345 ASP cc_start: 0.8121 (t0) cc_final: 0.7547 (t0) REVERT: E 349 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.7224 (mtt90) REVERT: A 311 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7401 (tmtt) REVERT: A 345 ASP cc_start: 0.8462 (t0) cc_final: 0.8183 (t0) REVERT: A 349 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.7517 (mmm-85) REVERT: A 379 ARG cc_start: 0.7551 (mmt180) cc_final: 0.7248 (mmm160) REVERT: B 345 ASP cc_start: 0.8028 (t0) cc_final: 0.7404 (t0) REVERT: B 347 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7946 (mmmm) REVERT: B 349 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7618 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3478 time to fit residues: 18.2948 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.120790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.094008 restraints weight = 4512.227| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.57 r_work: 0.3620 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3522 Z= 0.224 Angle : 0.564 4.110 4710 Z= 0.299 Chirality : 0.049 0.124 528 Planarity : 0.004 0.042 600 Dihedral : 4.837 12.606 468 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.25 % Allowed : 13.13 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.005 0.001 PHE C 378 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG F 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 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.448 Fit side-chains REVERT: F 311 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6829 (tmtt) REVERT: F 321 LYS cc_start: 0.7139 (mttt) cc_final: 0.6356 (ttpt) REVERT: F 340 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7359 (mtpt) REVERT: F 349 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.7163 (mtt90) REVERT: C 322 CYS cc_start: 0.8490 (t) cc_final: 0.8231 (m) REVERT: C 345 ASP cc_start: 0.8443 (t0) cc_final: 0.8127 (t0) REVERT: C 349 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7130 (mmm-85) REVERT: D 311 LYS cc_start: 0.7527 (ttpt) cc_final: 0.6534 (tppt) REVERT: D 345 ASP cc_start: 0.7989 (t0) cc_final: 0.7395 (t0) REVERT: E 311 LYS cc_start: 0.7269 (ttpt) cc_final: 0.6802 (tmtt) REVERT: E 345 ASP cc_start: 0.8107 (t0) cc_final: 0.7553 (t0) REVERT: E 349 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.7155 (mtt90) REVERT: A 322 CYS cc_start: 0.8501 (t) cc_final: 0.8172 (m) REVERT: A 345 ASP cc_start: 0.8458 (t0) cc_final: 0.8166 (t0) REVERT: A 349 ARG cc_start: 0.7746 (mtt-85) cc_final: 0.7479 (mmm-85) REVERT: A 379 ARG cc_start: 0.7592 (mmt180) cc_final: 0.7329 (mmm160) REVERT: B 345 ASP cc_start: 0.7967 (t0) cc_final: 0.7333 (t0) REVERT: B 347 LYS cc_start: 0.8227 (mmtp) cc_final: 0.7957 (mmmm) REVERT: B 349 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7601 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.3570 time to fit residues: 20.2494 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.4726 r_free = 0.4726 target = 0.258959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.203619 restraints weight = 3781.626| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.97 r_work: 0.3801 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.3480 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3522 Z= 0.164 Angle : 0.529 3.936 4710 Z= 0.278 Chirality : 0.048 0.128 528 Planarity : 0.005 0.040 600 Dihedral : 4.562 12.222 468 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 14.90 % 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: -4.59 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.017 0.001 PHE F 378 TYR 0.007 0.001 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 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.438 Fit side-chains REVERT: F 349 ARG cc_start: 0.7492 (mtt-85) cc_final: 0.7266 (mtt90) REVERT: C 345 ASP cc_start: 0.8513 (t0) cc_final: 0.8208 (t0) REVERT: C 349 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7159 (mmm-85) REVERT: D 311 LYS cc_start: 0.7678 (ttpt) cc_final: 0.6721 (tppt) REVERT: D 345 ASP cc_start: 0.8052 (t0) cc_final: 0.7493 (t0) REVERT: D 372 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7444 (mp0) REVERT: E 311 LYS cc_start: 0.7432 (ttpt) cc_final: 0.6930 (tmtt) REVERT: E 345 ASP cc_start: 0.8180 (t0) cc_final: 0.7628 (t0) REVERT: E 349 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7288 (mtt90) REVERT: A 322 CYS cc_start: 0.8496 (t) cc_final: 0.8233 (m) REVERT: A 345 ASP cc_start: 0.8478 (t0) cc_final: 0.8185 (t0) REVERT: A 349 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7533 (mmm-85) REVERT: A 379 ARG cc_start: 0.7637 (mmt180) cc_final: 0.7337 (mmm160) REVERT: B 311 LYS cc_start: 0.7645 (ttpt) cc_final: 0.6612 (tppt) REVERT: B 345 ASP cc_start: 0.7956 (t0) cc_final: 0.7321 (t0) REVERT: B 349 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7669 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3525 time to fit residues: 16.2530 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.0000 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 3.1992 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.115953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088366 restraints weight = 4552.638| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.63 r_work: 0.3599 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1791 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= 0.237 Angle : 0.561 4.011 4710 Z= 0.297 Chirality : 0.049 0.124 528 Planarity : 0.005 0.049 600 Dihedral : 4.717 12.424 468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.25 % Allowed : 14.65 % 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: -4.59 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.006 0.001 PHE C 378 TYR 0.008 0.002 TYR B 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.469 Fit side-chains REVERT: F 345 ASP cc_start: 0.8096 (t0) cc_final: 0.7774 (t0) REVERT: F 349 ARG cc_start: 0.7349 (mtt-85) cc_final: 0.7129 (mtt90) REVERT: C 345 ASP cc_start: 0.8461 (t0) cc_final: 0.8131 (t0) REVERT: C 349 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7076 (mmm-85) REVERT: D 311 LYS cc_start: 0.7651 (ttpt) cc_final: 0.6584 (tppt) REVERT: D 345 ASP cc_start: 0.8018 (t0) cc_final: 0.7454 (t0) REVERT: D 372 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7512 (mp0) REVERT: E 311 LYS cc_start: 0.7311 (ttpt) cc_final: 0.6801 (tmtt) REVERT: E 345 ASP cc_start: 0.8110 (t0) cc_final: 0.7547 (t0) REVERT: E 349 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.7136 (mtt90) REVERT: A 322 CYS cc_start: 0.8513 (t) cc_final: 0.8166 (m) REVERT: A 345 ASP cc_start: 0.8432 (t0) cc_final: 0.8133 (t0) REVERT: A 349 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7458 (mmm-85) REVERT: A 379 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7336 (mmm160) REVERT: B 311 LYS cc_start: 0.7456 (ttpt) cc_final: 0.6413 (tppt) REVERT: B 345 ASP cc_start: 0.7946 (t0) cc_final: 0.7308 (t0) REVERT: B 347 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7918 (mmmm) REVERT: B 349 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7606 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.3402 time to fit residues: 16.0973 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 : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.112505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085311 restraints weight = 4661.223| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.61 r_work: 0.3518 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3522 Z= 0.381 Angle : 0.644 4.439 4710 Z= 0.346 Chirality : 0.051 0.126 528 Planarity : 0.006 0.057 600 Dihedral : 5.212 12.934 468 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.51 % Allowed : 14.65 % Favored : 84.85 % 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 (0.31), 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 0.004 0.001 HIS C 362 PHE 0.018 0.003 PHE E 378 TYR 0.011 0.002 TYR B 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 311 LYS cc_start: 0.6974 (ttpt) cc_final: 0.6499 (tmtt) REVERT: F 321 LYS cc_start: 0.7100 (mttt) cc_final: 0.6383 (ttpt) REVERT: F 345 ASP cc_start: 0.8063 (t0) cc_final: 0.7775 (t0) REVERT: C 345 ASP cc_start: 0.8425 (t0) cc_final: 0.8123 (t0) REVERT: D 311 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6474 (tptt) REVERT: D 345 ASP cc_start: 0.8131 (t0) cc_final: 0.7457 (t0) REVERT: D 372 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7543 (mp0) REVERT: E 345 ASP cc_start: 0.8063 (t0) cc_final: 0.7318 (t0) REVERT: E 349 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.7195 (mtt90) REVERT: A 345 ASP cc_start: 0.8436 (t0) cc_final: 0.7865 (t0) REVERT: A 349 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7499 (mmm-85) REVERT: A 379 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7398 (mmm160) REVERT: B 345 ASP cc_start: 0.8042 (t0) cc_final: 0.7476 (t0) REVERT: B 349 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7613 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.3542 time to fit residues: 19.3480 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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: 6.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.115879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088204 restraints weight = 4593.859| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.65 r_work: 0.3591 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1920 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= 0.225 Angle : 0.570 4.165 4710 Z= 0.303 Chirality : 0.049 0.125 528 Planarity : 0.005 0.057 600 Dihedral : 4.862 12.791 468 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -4.51 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.018 0.002 PHE F 378 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG F 379 ********************** 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 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: F 311 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6612 (tmtt) REVERT: F 343 LYS cc_start: 0.6695 (mttt) cc_final: 0.6171 (mptt) REVERT: F 345 ASP cc_start: 0.8047 (t0) cc_final: 0.7664 (t0) REVERT: C 345 ASP cc_start: 0.8487 (t0) cc_final: 0.8154 (t0) REVERT: C 349 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7136 (mmm-85) REVERT: D 311 LYS cc_start: 0.7563 (ttpt) cc_final: 0.6417 (tppt) REVERT: D 345 ASP cc_start: 0.8069 (t0) cc_final: 0.7438 (t0) REVERT: D 372 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7559 (mp0) REVERT: E 311 LYS cc_start: 0.7296 (ttpt) cc_final: 0.6776 (tmtt) REVERT: E 345 ASP cc_start: 0.8058 (t0) cc_final: 0.7518 (t0) REVERT: E 349 ARG cc_start: 0.7503 (mtt-85) cc_final: 0.7163 (mtt90) REVERT: E 372 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7026 (mp0) REVERT: A 322 CYS cc_start: 0.8493 (t) cc_final: 0.8186 (m) REVERT: A 345 ASP cc_start: 0.8443 (t0) cc_final: 0.8155 (t0) REVERT: A 349 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7484 (mmm-85) REVERT: A 379 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7402 (mmm160) REVERT: B 311 LYS cc_start: 0.7512 (ttpt) cc_final: 0.6412 (tppt) REVERT: B 345 ASP cc_start: 0.7953 (t0) cc_final: 0.7335 (t0) REVERT: B 349 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7584 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.3539 time to fit residues: 20.8181 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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: 0.0670 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.2302 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.115564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.087953 restraints weight = 4604.127| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.64 r_work: 0.3589 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1966 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= 0.239 Angle : 0.570 4.206 4710 Z= 0.303 Chirality : 0.049 0.124 528 Planarity : 0.005 0.056 600 Dihedral : 4.820 12.797 468 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % 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: -4.49 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.24), 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 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.36 seconds wall clock time: 39 minutes 10.16 seconds (2350.16 seconds total)