Starting phenix.real_space_refine on Thu Mar 6 04:09:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukj_20806/03_2025/6ukj_20806_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukj_20806/03_2025/6ukj_20806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2025/6ukj_20806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2025/6ukj_20806.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2025/6ukj_20806_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2025/6ukj_20806_neut.cif" } resolution = 3.3 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= 1.000 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 28 5.16 5 C 3037 2.51 5 N 723 2.21 5 O 837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4625 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2810 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.97, per 1000 atoms: 0.86 Number of scatterers: 4625 At special positions: 0 Unit cell: (63.135, 84.87, 99.36, 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 28 16.00 O 837 8.00 N 723 7.00 C 3037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 312 " distance=2.02 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 309 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 555.0 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 48.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.232A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.858A pdb=" N MET A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 112 Processing helix chain 'A' and resid 126 through 148 Processing helix chain 'A' and resid 152 through 174 removed outlier: 3.949A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 180 through 205 removed outlier: 3.915A pdb=" N GLU A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.598A pdb=" N TYR A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 314 through 340 removed outlier: 4.388A pdb=" N THR A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.753A pdb=" N ILE A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 removed outlier: 3.622A pdb=" N ALA A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 404 removed outlier: 3.692A pdb=" N PHE A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.502A pdb=" N TYR H 34 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 35' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.804A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.622A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP H 76 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.904A pdb=" N CYS H 99 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP H 122 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG H 101 " --> pdb=" O ASP H 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 50 Processing sheet with id=AA4, first strand: chain 'H' and resid 52 through 55 Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.535A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.550A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 786 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: 1.45 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 711 1.32 - 1.44: 1397 1.44 - 1.57: 2590 1.57 - 1.69: 1 1.69 - 1.81: 41 Bond restraints: 4740 Sorted by residual: bond pdb=" C PRO L 9 " pdb=" O PRO L 9 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 8.98e+00 bond pdb=" CA SER L 10 " pdb=" CB SER L 10 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.55e-02 4.16e+03 6.64e+00 bond pdb=" N GLN L 7 " pdb=" CA GLN L 7 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N SER L 8 " pdb=" CA SER L 8 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.07e+00 bond pdb=" CA SER L 11 " pdb=" CB SER L 11 " ideal model delta sigma weight residual 1.534 1.492 0.042 1.72e-02 3.38e+03 5.85e+00 ... (remaining 4735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 6170 1.92 - 3.85: 222 3.85 - 5.77: 33 5.77 - 7.70: 11 7.70 - 9.62: 4 Bond angle restraints: 6440 Sorted by residual: angle pdb=" N PRO L 9 " pdb=" CA PRO L 9 " pdb=" C PRO L 9 " ideal model delta sigma weight residual 112.47 104.55 7.92 2.06e+00 2.36e-01 1.48e+01 angle pdb=" C GLN L 7 " pdb=" N SER L 8 " pdb=" CA SER L 8 " ideal model delta sigma weight residual 121.80 130.34 -8.54 2.44e+00 1.68e-01 1.22e+01 angle pdb=" O GLN L 7 " pdb=" C GLN L 7 " pdb=" N SER L 8 " ideal model delta sigma weight residual 123.22 126.77 -3.55 1.14e+00 7.69e-01 9.70e+00 angle pdb=" CB GLN L 7 " pdb=" CG GLN L 7 " pdb=" CD GLN L 7 " ideal model delta sigma weight residual 112.60 107.55 5.05 1.70e+00 3.46e-01 8.84e+00 angle pdb=" C ILE A 260 " pdb=" CA ILE A 260 " pdb=" CB ILE A 260 " ideal model delta sigma weight residual 112.26 107.55 4.71 1.62e+00 3.81e-01 8.45e+00 ... (remaining 6435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 2502 16.66 - 33.33: 244 33.33 - 49.99: 56 49.99 - 66.65: 8 66.65 - 83.31: 2 Dihedral angle restraints: 2812 sinusoidal: 1106 harmonic: 1706 Sorted by residual: dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual -86.00 -154.46 68.46 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 44.16 48.84 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA LEU A 175 " pdb=" C LEU A 175 " pdb=" N ARG A 176 " pdb=" CA ARG A 176 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 654 0.076 - 0.152: 78 0.152 - 0.228: 4 0.228 - 0.305: 2 0.305 - 0.381: 1 Chirality restraints: 739 Sorted by residual: chirality pdb=" CBG Y01 A 501 " pdb=" CAQ Y01 A 501 " pdb=" CBD Y01 A 501 " pdb=" CBI Y01 A 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CBF Y01 A 501 " pdb=" CAS Y01 A 501 " pdb=" CBD Y01 A 501 " pdb=" CBH Y01 A 501 " both_signs ideal model delta sigma weight residual False -2.45 -2.71 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO L 9 " pdb=" N PRO L 9 " pdb=" C PRO L 9 " pdb=" CB PRO L 9 " both_signs ideal model delta sigma weight residual False 2.72 2.97 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 736 not shown) Planarity restraints: 788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 8 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C SER L 8 " 0.041 2.00e-02 2.50e+03 pdb=" O SER L 8 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO L 9 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 95 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO L 96 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER L 11 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C SER L 11 " -0.030 2.00e-02 2.50e+03 pdb=" O SER L 11 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU L 12 " 0.010 2.00e-02 2.50e+03 ... (remaining 785 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 86 2.67 - 3.23: 4571 3.23 - 3.79: 7169 3.79 - 4.34: 9760 4.34 - 4.90: 16423 Nonbonded interactions: 38009 Sorted by model distance: nonbonded pdb=" O ILE A 347 " pdb=" OH TYR A 384 " model vdw 2.114 3.040 nonbonded pdb=" OG SER A 72 " pdb=" OE1 GLN A 352 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 157 " pdb=" OE2 GLU A 198 " model vdw 2.260 3.040 nonbonded pdb=" OG SER L 8 " pdb=" CD PRO L 9 " model vdw 2.262 3.440 nonbonded pdb=" OE2 GLU A 208 " pdb=" NZ LYS A 270 " model vdw 2.284 3.120 ... (remaining 38004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.320 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.058 4740 Z= 0.456 Angle : 0.907 9.621 6440 Z= 0.477 Chirality : 0.052 0.381 739 Planarity : 0.005 0.047 788 Dihedral : 13.739 83.312 1708 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % Rotamer: Outliers : 0.79 % Allowed : 5.95 % Favored : 93.25 % 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: -3.21 (0.28), residues: 574 helix: -1.69 (0.25), residues: 263 sheet: -1.94 (0.47), residues: 93 loop : -2.58 (0.34), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 95 HIS 0.006 0.001 HIS H 38 PHE 0.018 0.002 PHE A 251 TYR 0.019 0.002 TYR H 102 ARG 0.013 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8051 (ptpt) REVERT: A 218 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8237 (mp) REVERT: A 307 LYS cc_start: 0.8745 (mptt) cc_final: 0.8526 (mmtt) REVERT: A 347 ILE cc_start: 0.8027 (mm) cc_final: 0.7775 (mt) REVERT: A 384 TYR cc_start: 0.8336 (t80) cc_final: 0.7693 (t80) REVERT: A 397 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6664 (mp) REVERT: H 68 LYS cc_start: 0.8338 (tttt) cc_final: 0.7973 (ttpp) REVERT: H 80 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0) REVERT: L 56 TYR cc_start: 0.8449 (t80) cc_final: 0.8003 (t80) outliers start: 4 outliers final: 2 residues processed: 129 average time/residue: 0.2203 time to fit residues: 34.3395 Evaluate side-chains 103 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain L residue 10 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113109 restraints weight = 7599.489| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.94 r_work: 0.3274 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4740 Z= 0.206 Angle : 0.597 7.221 6440 Z= 0.315 Chirality : 0.042 0.169 739 Planarity : 0.004 0.043 788 Dihedral : 7.837 57.512 710 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.78 % Allowed : 11.71 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.32), residues: 574 helix: -0.12 (0.30), residues: 266 sheet: -1.17 (0.51), residues: 91 loop : -2.16 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 95 HIS 0.003 0.001 HIS A 97 PHE 0.015 0.001 PHE A 268 TYR 0.014 0.001 TYR A 345 ARG 0.007 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7859 (t80) cc_final: 0.6937 (m-10) REVERT: A 310 ASP cc_start: 0.8748 (p0) cc_final: 0.8460 (p0) REVERT: A 333 THR cc_start: 0.8952 (m) cc_final: 0.8710 (m) REVERT: A 347 ILE cc_start: 0.8638 (mm) cc_final: 0.8189 (mt) REVERT: A 384 TYR cc_start: 0.8939 (t80) cc_final: 0.8651 (t80) REVERT: H 68 LYS cc_start: 0.8448 (tttt) cc_final: 0.8014 (ttpp) REVERT: H 80 ASN cc_start: 0.8650 (t0) cc_final: 0.8354 (t0) REVERT: L 56 TYR cc_start: 0.8856 (t80) cc_final: 0.8516 (t80) REVERT: L 91 GLN cc_start: 0.9116 (pp30) cc_final: 0.8182 (pp30) outliers start: 14 outliers final: 10 residues processed: 134 average time/residue: 0.1817 time to fit residues: 30.3460 Evaluate side-chains 118 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 50 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115125 restraints weight = 7675.282| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.92 r_work: 0.3305 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4740 Z= 0.184 Angle : 0.558 7.170 6440 Z= 0.293 Chirality : 0.042 0.147 739 Planarity : 0.004 0.041 788 Dihedral : 7.010 59.554 705 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.17 % Allowed : 14.88 % Favored : 80.95 % 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: -0.84 (0.34), residues: 574 helix: 0.56 (0.31), residues: 269 sheet: -0.82 (0.54), residues: 91 loop : -1.84 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 PHE 0.014 0.001 PHE A 251 TYR 0.011 0.001 TYR A 345 ARG 0.006 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8310 (mm-30) REVERT: A 305 MET cc_start: 0.8667 (mtp) cc_final: 0.8316 (mmm) REVERT: A 310 ASP cc_start: 0.8677 (p0) cc_final: 0.8403 (p0) REVERT: A 325 PHE cc_start: 0.9127 (m-10) cc_final: 0.8877 (m-80) REVERT: A 333 THR cc_start: 0.9102 (m) cc_final: 0.8817 (m) REVERT: A 347 ILE cc_start: 0.8607 (mm) cc_final: 0.8197 (mt) REVERT: A 384 TYR cc_start: 0.8937 (t80) cc_final: 0.8607 (t80) REVERT: H 38 HIS cc_start: 0.8349 (p90) cc_final: 0.8094 (p-80) REVERT: H 68 LYS cc_start: 0.8394 (tttt) cc_final: 0.8012 (ttpp) REVERT: H 80 ASN cc_start: 0.8576 (t0) cc_final: 0.8261 (t0) REVERT: L 18 ASP cc_start: 0.8176 (m-30) cc_final: 0.7898 (m-30) REVERT: L 56 TYR cc_start: 0.8901 (t80) cc_final: 0.8645 (t80) REVERT: L 91 GLN cc_start: 0.9190 (pp30) cc_final: 0.8301 (pp30) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.1840 time to fit residues: 29.8602 Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.120525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112339 restraints weight = 7777.895| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.92 r_work: 0.3265 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4740 Z= 0.215 Angle : 0.604 11.254 6440 Z= 0.309 Chirality : 0.042 0.158 739 Planarity : 0.004 0.041 788 Dihedral : 6.968 58.849 705 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.56 % Allowed : 16.67 % Favored : 78.77 % 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: -0.43 (0.35), residues: 574 helix: 0.92 (0.31), residues: 269 sheet: -0.69 (0.56), residues: 91 loop : -1.62 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 95 HIS 0.003 0.001 HIS H 38 PHE 0.020 0.001 PHE A 268 TYR 0.014 0.001 TYR A 345 ARG 0.007 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7818 (t80) cc_final: 0.6911 (m-10) REVERT: A 325 PHE cc_start: 0.9141 (m-10) cc_final: 0.8894 (m-80) REVERT: A 333 THR cc_start: 0.9123 (m) cc_final: 0.8809 (m) REVERT: A 347 ILE cc_start: 0.8760 (mm) cc_final: 0.8447 (mt) REVERT: A 384 TYR cc_start: 0.8988 (t80) cc_final: 0.8611 (t80) REVERT: H 49 GLU cc_start: 0.8345 (tt0) cc_final: 0.8088 (tt0) REVERT: H 68 LYS cc_start: 0.8401 (tttt) cc_final: 0.8061 (ttpp) REVERT: H 80 ASN cc_start: 0.8492 (t0) cc_final: 0.8186 (t0) REVERT: L 56 TYR cc_start: 0.8951 (t80) cc_final: 0.8624 (t80) REVERT: L 91 GLN cc_start: 0.9238 (pp30) cc_final: 0.8160 (pp30) outliers start: 23 outliers final: 22 residues processed: 124 average time/residue: 0.1756 time to fit residues: 27.4161 Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.0570 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 214 ASN L 39 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118832 restraints weight = 7810.932| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.97 r_work: 0.3360 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4740 Z= 0.145 Angle : 0.551 10.480 6440 Z= 0.281 Chirality : 0.040 0.130 739 Planarity : 0.004 0.043 788 Dihedral : 6.611 59.761 705 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.17 % Allowed : 17.86 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.35), residues: 574 helix: 1.23 (0.31), residues: 272 sheet: -0.60 (0.57), residues: 91 loop : -1.41 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 109 HIS 0.002 0.001 HIS A 97 PHE 0.018 0.001 PHE A 268 TYR 0.008 0.001 TYR H 102 ARG 0.005 0.000 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7750 (t80) cc_final: 0.6793 (m-80) REVERT: A 333 THR cc_start: 0.9098 (m) cc_final: 0.8805 (m) REVERT: A 347 ILE cc_start: 0.8569 (mm) cc_final: 0.8262 (mt) REVERT: A 384 TYR cc_start: 0.8925 (t80) cc_final: 0.8669 (t80) REVERT: H 49 GLU cc_start: 0.8340 (tt0) cc_final: 0.8122 (tt0) REVERT: H 68 LYS cc_start: 0.8304 (tttt) cc_final: 0.7900 (ttpp) REVERT: H 80 ASN cc_start: 0.8503 (t0) cc_final: 0.8190 (t0) REVERT: L 18 ASP cc_start: 0.8119 (m-30) cc_final: 0.7829 (m-30) REVERT: L 56 TYR cc_start: 0.8891 (t80) cc_final: 0.8554 (t80) REVERT: L 73 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8610 (p) outliers start: 21 outliers final: 18 residues processed: 141 average time/residue: 0.1733 time to fit residues: 30.8297 Evaluate side-chains 131 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115354 restraints weight = 7828.994| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.96 r_work: 0.3309 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4740 Z= 0.183 Angle : 0.564 6.760 6440 Z= 0.292 Chirality : 0.041 0.139 739 Planarity : 0.004 0.040 788 Dihedral : 6.574 59.859 705 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.16 % Allowed : 19.25 % Favored : 75.60 % 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: 0.11 (0.35), residues: 574 helix: 1.36 (0.32), residues: 272 sheet: -0.46 (0.58), residues: 90 loop : -1.37 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE A 268 TYR 0.012 0.001 TYR A 345 ARG 0.008 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7780 (t80) cc_final: 0.6799 (m-80) REVERT: A 305 MET cc_start: 0.8655 (mtp) cc_final: 0.8401 (mmm) REVERT: A 333 THR cc_start: 0.9117 (m) cc_final: 0.8815 (m) REVERT: A 347 ILE cc_start: 0.8662 (mm) cc_final: 0.8351 (mt) REVERT: A 384 TYR cc_start: 0.8996 (t80) cc_final: 0.8683 (t80) REVERT: H 49 GLU cc_start: 0.8442 (tt0) cc_final: 0.8196 (tt0) REVERT: H 68 LYS cc_start: 0.8343 (tttt) cc_final: 0.7926 (ttpp) REVERT: H 76 ASP cc_start: 0.8142 (m-30) cc_final: 0.7931 (m-30) REVERT: H 80 ASN cc_start: 0.8484 (t0) cc_final: 0.8205 (t0) REVERT: L 3 ILE cc_start: 0.8468 (mt) cc_final: 0.7592 (mt) REVERT: L 56 TYR cc_start: 0.8923 (t80) cc_final: 0.8600 (t80) REVERT: L 73 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8605 (p) outliers start: 26 outliers final: 21 residues processed: 129 average time/residue: 0.1711 time to fit residues: 27.8539 Evaluate side-chains 129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112682 restraints weight = 7844.507| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.96 r_work: 0.3270 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4740 Z= 0.217 Angle : 0.593 7.715 6440 Z= 0.306 Chirality : 0.042 0.152 739 Planarity : 0.004 0.044 788 Dihedral : 6.658 57.563 705 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.56 % Allowed : 19.44 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.35), residues: 574 helix: 1.33 (0.32), residues: 273 sheet: -0.46 (0.57), residues: 90 loop : -1.34 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.008 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.9136 (m) cc_final: 0.8834 (m) REVERT: A 384 TYR cc_start: 0.9031 (t80) cc_final: 0.8695 (t80) REVERT: H 49 GLU cc_start: 0.8442 (tt0) cc_final: 0.8169 (tt0) REVERT: H 68 LYS cc_start: 0.8358 (tttt) cc_final: 0.7960 (ttpp) REVERT: H 80 ASN cc_start: 0.8483 (t0) cc_final: 0.8221 (t0) REVERT: L 56 TYR cc_start: 0.8956 (t80) cc_final: 0.8614 (t80) REVERT: L 91 GLN cc_start: 0.9211 (pp30) cc_final: 0.8340 (pp30) outliers start: 28 outliers final: 23 residues processed: 129 average time/residue: 0.1668 time to fit residues: 27.1215 Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.0070 chunk 56 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.124625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116385 restraints weight = 7799.011| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.97 r_work: 0.3329 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4740 Z= 0.168 Angle : 0.563 6.476 6440 Z= 0.292 Chirality : 0.041 0.129 739 Planarity : 0.004 0.042 788 Dihedral : 6.552 58.263 705 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.96 % Allowed : 20.24 % Favored : 74.80 % 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: 0.32 (0.36), residues: 574 helix: 1.50 (0.32), residues: 272 sheet: -0.39 (0.57), residues: 90 loop : -1.18 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 PHE 0.016 0.001 PHE A 268 TYR 0.009 0.001 TYR L 87 ARG 0.008 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7791 (t80) cc_final: 0.6841 (m-80) REVERT: A 271 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7492 (mm-40) REVERT: A 305 MET cc_start: 0.8785 (mmm) cc_final: 0.8500 (mtp) REVERT: A 333 THR cc_start: 0.9113 (m) cc_final: 0.8817 (m) REVERT: A 384 TYR cc_start: 0.9022 (t80) cc_final: 0.8714 (t80) REVERT: H 49 GLU cc_start: 0.8364 (tt0) cc_final: 0.8110 (tt0) REVERT: H 68 LYS cc_start: 0.8359 (tttt) cc_final: 0.7922 (ttpp) REVERT: H 80 ASN cc_start: 0.8478 (t0) cc_final: 0.8190 (t0) REVERT: L 56 TYR cc_start: 0.8923 (t80) cc_final: 0.8591 (t80) REVERT: L 73 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8597 (p) outliers start: 25 outliers final: 22 residues processed: 131 average time/residue: 0.2230 time to fit residues: 36.8364 Evaluate side-chains 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113316 restraints weight = 7833.400| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.00 r_work: 0.3283 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4740 Z= 0.220 Angle : 0.604 10.128 6440 Z= 0.308 Chirality : 0.042 0.151 739 Planarity : 0.004 0.041 788 Dihedral : 6.597 57.627 705 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.56 % Allowed : 20.63 % Favored : 73.81 % 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: 0.24 (0.35), residues: 574 helix: 1.41 (0.32), residues: 273 sheet: -0.34 (0.58), residues: 90 loop : -1.26 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 95 HIS 0.003 0.001 HIS H 38 PHE 0.016 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.005 0.000 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.9031 (mtp85) cc_final: 0.8751 (mtp85) REVERT: A 271 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7595 (mm-40) REVERT: A 305 MET cc_start: 0.8858 (mmm) cc_final: 0.8491 (mtp) REVERT: A 333 THR cc_start: 0.9134 (m) cc_final: 0.8831 (m) REVERT: A 384 TYR cc_start: 0.9034 (t80) cc_final: 0.8696 (t80) REVERT: A 395 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8539 (t0) REVERT: H 49 GLU cc_start: 0.8403 (tt0) cc_final: 0.8139 (tt0) REVERT: H 68 LYS cc_start: 0.8420 (tttt) cc_final: 0.7967 (ttpp) REVERT: H 80 ASN cc_start: 0.8476 (t0) cc_final: 0.8185 (t0) REVERT: H 102 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8255 (m-10) REVERT: L 56 TYR cc_start: 0.8960 (t80) cc_final: 0.8630 (t80) outliers start: 28 outliers final: 25 residues processed: 129 average time/residue: 0.2454 time to fit residues: 40.3143 Evaluate side-chains 136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113645 restraints weight = 7755.210| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.97 r_work: 0.3288 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4740 Z= 0.207 Angle : 0.586 7.277 6440 Z= 0.303 Chirality : 0.042 0.147 739 Planarity : 0.004 0.041 788 Dihedral : 6.599 59.387 705 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.75 % Allowed : 20.63 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.35), residues: 574 helix: 1.41 (0.32), residues: 273 sheet: -0.27 (0.59), residues: 90 loop : -1.22 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE A 268 TYR 0.012 0.001 TYR A 360 ARG 0.006 0.000 ARG H 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.9024 (mtp85) cc_final: 0.8769 (mtp85) REVERT: A 271 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7564 (mm-40) REVERT: A 305 MET cc_start: 0.8865 (mmm) cc_final: 0.8521 (mtp) REVERT: A 333 THR cc_start: 0.9124 (m) cc_final: 0.8822 (m) REVERT: A 384 TYR cc_start: 0.9038 (t80) cc_final: 0.8684 (t80) REVERT: H 49 GLU cc_start: 0.8380 (tt0) cc_final: 0.8117 (tt0) REVERT: H 68 LYS cc_start: 0.8406 (tttt) cc_final: 0.7961 (ttpp) REVERT: H 80 ASN cc_start: 0.8469 (t0) cc_final: 0.8179 (t0) REVERT: L 56 TYR cc_start: 0.8960 (t80) cc_final: 0.8621 (t80) outliers start: 29 outliers final: 26 residues processed: 127 average time/residue: 0.2686 time to fit residues: 43.4091 Evaluate side-chains 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112473 restraints weight = 7851.402| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.98 r_work: 0.3270 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4740 Z= 0.224 Angle : 0.590 7.262 6440 Z= 0.305 Chirality : 0.042 0.149 739 Planarity : 0.004 0.041 788 Dihedral : 6.631 58.499 705 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.75 % Allowed : 21.03 % Favored : 73.21 % 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: 0.24 (0.35), residues: 574 helix: 1.38 (0.32), residues: 273 sheet: -0.28 (0.58), residues: 90 loop : -1.25 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE A 268 TYR 0.014 0.001 TYR A 345 ARG 0.009 0.000 ARG H 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2732.19 seconds wall clock time: 49 minutes 20.55 seconds (2960.55 seconds total)