Starting phenix.real_space_refine on Thu Jul 24 00:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukj_20806/07_2025/6ukj_20806_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukj_20806/07_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_20806/07_2025/6ukj_20806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukj_20806/07_2025/6ukj_20806.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukj_20806/07_2025/6ukj_20806_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukj_20806/07_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-5711/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: 3.58, per 1000 atoms: 0.77 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: 1.21 Conformation dependent library (CDL) restraints added in 546.0 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: 0.53 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: 1.19 Time building geometry restraints manager: 1.39 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: 2.010 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.360 Find NCS groups from input model: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- 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 4745 Z= 0.323 Angle : 0.908 9.621 6448 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 Details of bonding type rmsd hydrogen bonds : bond 0.10853 ( 263) hydrogen bonds : angle 5.64310 ( 786) SS BOND : bond 0.00839 ( 4) SS BOND : angle 1.62881 ( 8) covalent geometry : bond 0.00712 ( 4740) covalent geometry : angle 0.90716 ( 6440) Misc. bond : bond 0.03126 ( 1) *********************** 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 : 0.505 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: 0.2118 time to fit residues: 32.8450 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 : 0.507 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 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: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.121363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112929 restraints weight = 7622.699| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.93 r_work: 0.3269 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4745 Z= 0.154 Angle : 0.602 7.258 6448 Z= 0.317 Chirality : 0.043 0.171 739 Planarity : 0.004 0.043 788 Dihedral : 7.824 56.807 710 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.78 % Allowed : 11.90 % Favored : 85.32 % 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: -1.61 (0.32), residues: 574 helix: -0.11 (0.30), residues: 266 sheet: -1.16 (0.51), residues: 91 loop : -2.16 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 263) hydrogen bonds : angle 4.66892 ( 786) SS BOND : bond 0.00335 ( 4) SS BOND : angle 1.21563 ( 8) covalent geometry : bond 0.00337 ( 4740) covalent geometry : angle 0.60097 ( 6440) Misc. bond : bond 0.00067 ( 1) *********************** 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 : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7892 (t80) cc_final: 0.6966 (m-10) REVERT: A 305 MET cc_start: 0.8772 (mmm) cc_final: 0.8527 (mtp) REVERT: A 310 ASP cc_start: 0.8749 (p0) cc_final: 0.8464 (p0) REVERT: A 333 THR cc_start: 0.8961 (m) cc_final: 0.8728 (m) REVERT: A 347 ILE cc_start: 0.8662 (mm) cc_final: 0.8215 (mt) REVERT: A 384 TYR cc_start: 0.8950 (t80) cc_final: 0.8672 (t80) REVERT: H 68 LYS cc_start: 0.8452 (tttt) cc_final: 0.8021 (ttpp) REVERT: H 80 ASN cc_start: 0.8562 (t0) cc_final: 0.8253 (t0) REVERT: L 3 ILE cc_start: 0.8175 (mt) cc_final: 0.7259 (mt) REVERT: L 56 TYR cc_start: 0.8874 (t80) cc_final: 0.8515 (t80) REVERT: L 91 GLN cc_start: 0.9126 (pp30) cc_final: 0.8232 (pp30) outliers start: 14 outliers final: 10 residues processed: 134 average time/residue: 0.1739 time to fit residues: 29.1152 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 : 0.542 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 28 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 183 ASN A 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112723 restraints weight = 7741.446| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.92 r_work: 0.3276 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4745 Z= 0.150 Angle : 0.579 7.797 6448 Z= 0.304 Chirality : 0.042 0.167 739 Planarity : 0.004 0.040 788 Dihedral : 7.101 58.849 705 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.56 % Allowed : 14.88 % Favored : 80.56 % 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: -0.87 (0.34), residues: 574 helix: 0.53 (0.31), residues: 269 sheet: -0.83 (0.54), residues: 91 loop : -1.85 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 PHE 0.013 0.001 PHE A 251 TYR 0.013 0.001 TYR A 345 ARG 0.007 0.001 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 263) hydrogen bonds : angle 4.52730 ( 786) SS BOND : bond 0.00370 ( 4) SS BOND : angle 1.09779 ( 8) covalent geometry : bond 0.00334 ( 4740) covalent geometry : angle 0.57853 ( 6440) Misc. bond : bond 0.00051 ( 1) *********************** 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 133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7852 (t80) cc_final: 0.6908 (m-10) REVERT: A 299 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 333 THR cc_start: 0.9079 (m) cc_final: 0.8812 (m) REVERT: A 347 ILE cc_start: 0.8734 (mm) cc_final: 0.8400 (mt) REVERT: A 384 TYR cc_start: 0.8959 (t80) cc_final: 0.8554 (t80) REVERT: H 38 HIS cc_start: 0.8560 (p90) cc_final: 0.8335 (p-80) REVERT: H 68 LYS cc_start: 0.8437 (tttt) cc_final: 0.8046 (ttpp) REVERT: H 80 ASN cc_start: 0.8623 (t0) cc_final: 0.8309 (t0) REVERT: L 56 TYR cc_start: 0.8928 (t80) cc_final: 0.8670 (t80) REVERT: L 91 GLN cc_start: 0.9207 (pp30) cc_final: 0.8360 (pp30) outliers start: 23 outliers final: 19 residues processed: 125 average time/residue: 0.1798 time to fit residues: 28.2044 Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE 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 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113533 restraints weight = 7760.704| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.94 r_work: 0.3286 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4745 Z= 0.135 Angle : 0.589 10.938 6448 Z= 0.301 Chirality : 0.042 0.147 739 Planarity : 0.004 0.041 788 Dihedral : 6.954 59.170 705 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.97 % Allowed : 17.06 % Favored : 78.97 % 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: -0.47 (0.35), residues: 574 helix: 0.92 (0.31), residues: 269 sheet: -0.73 (0.56), residues: 91 loop : -1.68 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 PHE 0.023 0.001 PHE A 268 TYR 0.012 0.001 TYR A 345 ARG 0.003 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 263) hydrogen bonds : angle 4.46541 ( 786) SS BOND : bond 0.00397 ( 4) SS BOND : angle 1.06220 ( 8) covalent geometry : bond 0.00294 ( 4740) covalent geometry : angle 0.58855 ( 6440) Misc. bond : bond 0.00038 ( 1) *********************** 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 137 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.9144 (m-10) cc_final: 0.8918 (m-80) REVERT: A 333 THR cc_start: 0.9106 (m) cc_final: 0.8794 (m) REVERT: A 347 ILE cc_start: 0.8757 (mm) cc_final: 0.8399 (mt) REVERT: A 384 TYR cc_start: 0.8986 (t80) cc_final: 0.8655 (t80) REVERT: H 49 GLU cc_start: 0.8372 (tt0) cc_final: 0.8118 (tt0) REVERT: H 68 LYS cc_start: 0.8401 (tttt) cc_final: 0.8025 (ttpp) REVERT: H 80 ASN cc_start: 0.8531 (t0) cc_final: 0.8234 (t0) REVERT: L 56 TYR cc_start: 0.8957 (t80) cc_final: 0.8607 (t80) REVERT: L 91 GLN cc_start: 0.9219 (pp30) cc_final: 0.8336 (pp30) outliers start: 20 outliers final: 20 residues processed: 131 average time/residue: 0.1770 time to fit residues: 29.3002 Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114753 restraints weight = 7871.791| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.94 r_work: 0.3304 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4745 Z= 0.129 Angle : 0.577 9.565 6448 Z= 0.296 Chirality : 0.041 0.143 739 Planarity : 0.004 0.047 788 Dihedral : 6.816 59.277 705 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.76 % Allowed : 17.86 % Favored : 77.38 % 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: -0.18 (0.35), residues: 574 helix: 1.14 (0.32), residues: 272 sheet: -0.60 (0.56), residues: 90 loop : -1.55 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 PHE 0.017 0.001 PHE A 268 TYR 0.012 0.001 TYR A 62 ARG 0.008 0.001 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 263) hydrogen bonds : angle 4.40626 ( 786) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.02207 ( 8) covalent geometry : bond 0.00281 ( 4740) covalent geometry : angle 0.57606 ( 6440) Misc. bond : bond 0.00033 ( 1) *********************** 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 141 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.9128 (m) cc_final: 0.8829 (m) REVERT: A 347 ILE cc_start: 0.8704 (mm) cc_final: 0.8376 (mt) REVERT: A 384 TYR cc_start: 0.9009 (t80) cc_final: 0.8683 (t80) REVERT: H 49 GLU cc_start: 0.8401 (tt0) cc_final: 0.8163 (tt0) REVERT: H 68 LYS cc_start: 0.8374 (tttt) cc_final: 0.7978 (ttpp) REVERT: H 80 ASN cc_start: 0.8536 (t0) cc_final: 0.8213 (t0) REVERT: L 18 ASP cc_start: 0.8114 (m-30) cc_final: 0.7914 (m-30) REVERT: L 56 TYR cc_start: 0.8962 (t80) cc_final: 0.8585 (t80) REVERT: L 73 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8576 (p) REVERT: L 91 GLN cc_start: 0.9220 (pp30) cc_final: 0.8489 (pp30) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.1815 time to fit residues: 30.5617 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 : 0.479 ------------------------------------------------------------------------------- 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 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 21 THR 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.124300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116049 restraints weight = 7851.296| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.97 r_work: 0.3323 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4745 Z= 0.119 Angle : 0.572 7.971 6448 Z= 0.292 Chirality : 0.041 0.148 739 Planarity : 0.004 0.047 788 Dihedral : 6.661 59.848 705 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.37 % Allowed : 19.25 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.35), residues: 574 helix: 1.31 (0.32), residues: 272 sheet: -0.46 (0.57), residues: 90 loop : -1.46 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 PHE 0.016 0.001 PHE A 268 TYR 0.010 0.001 TYR A 345 ARG 0.008 0.001 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 263) hydrogen bonds : angle 4.33161 ( 786) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.02849 ( 8) covalent geometry : bond 0.00256 ( 4740) covalent geometry : angle 0.57083 ( 6440) Misc. bond : bond 0.00026 ( 1) *********************** 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 142 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7759 (t80) cc_final: 0.6813 (m-80) REVERT: A 333 THR cc_start: 0.9117 (m) cc_final: 0.8815 (m) REVERT: A 347 ILE cc_start: 0.8627 (mm) cc_final: 0.8340 (mt) REVERT: A 384 TYR cc_start: 0.8982 (t80) cc_final: 0.8666 (t80) REVERT: H 49 GLU cc_start: 0.8388 (tt0) cc_final: 0.8138 (tt0) REVERT: H 68 LYS cc_start: 0.8370 (tttt) cc_final: 0.7937 (ttpp) REVERT: H 80 ASN cc_start: 0.8515 (t0) cc_final: 0.8211 (t0) REVERT: L 18 ASP cc_start: 0.8089 (m-30) cc_final: 0.7859 (m-30) REVERT: L 56 TYR cc_start: 0.8941 (t80) cc_final: 0.8608 (t80) REVERT: L 73 THR cc_start: 0.8960 (m) cc_final: 0.8606 (p) REVERT: L 91 GLN cc_start: 0.9215 (pp30) cc_final: 0.8415 (pp30) outliers start: 22 outliers final: 20 residues processed: 134 average time/residue: 0.1897 time to fit residues: 32.2816 Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 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 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 10 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.121281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113009 restraints weight = 7806.229| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.96 r_work: 0.3279 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4745 Z= 0.145 Angle : 0.590 7.370 6448 Z= 0.304 Chirality : 0.042 0.157 739 Planarity : 0.004 0.046 788 Dihedral : 6.649 58.150 705 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.36 % Allowed : 19.25 % Favored : 75.40 % 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: 1.31 (0.32), residues: 273 sheet: -0.49 (0.57), residues: 90 loop : -1.41 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 263) hydrogen bonds : angle 4.41319 ( 786) SS BOND : bond 0.00365 ( 4) SS BOND : angle 1.00934 ( 8) covalent geometry : bond 0.00322 ( 4740) covalent geometry : angle 0.58956 ( 6440) Misc. bond : bond 0.00033 ( 1) *********************** 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 138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: A 305 MET cc_start: 0.8713 (mtp) cc_final: 0.8235 (mmm) REVERT: A 333 THR cc_start: 0.9136 (m) cc_final: 0.8832 (m) REVERT: A 384 TYR cc_start: 0.9017 (t80) cc_final: 0.8661 (t80) REVERT: H 49 GLU cc_start: 0.8437 (tt0) cc_final: 0.8175 (tt0) REVERT: H 68 LYS cc_start: 0.8379 (tttt) cc_final: 0.7957 (ttpp) REVERT: H 80 ASN cc_start: 0.8498 (t0) cc_final: 0.8217 (t0) REVERT: L 18 ASP cc_start: 0.8186 (m-30) cc_final: 0.7904 (m-30) REVERT: L 56 TYR cc_start: 0.8985 (t80) cc_final: 0.8610 (t80) REVERT: L 73 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8584 (p) REVERT: L 91 GLN cc_start: 0.9252 (pp30) cc_final: 0.8438 (pp30) outliers start: 27 outliers final: 22 residues processed: 126 average time/residue: 0.2228 time to fit residues: 36.7023 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 : 1.177 ------------------------------------------------------------------------------- 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 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 7 GLN Chi-restraints excluded: chain L residue 10 SER 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: 1.9990 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.121270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112982 restraints weight = 7777.281| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.97 r_work: 0.3277 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4745 Z= 0.144 Angle : 0.587 6.869 6448 Z= 0.303 Chirality : 0.042 0.154 739 Planarity : 0.004 0.046 788 Dihedral : 6.653 56.477 705 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.16 % Allowed : 20.83 % Favored : 74.01 % 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: 1.35 (0.32), residues: 273 sheet: -0.49 (0.57), residues: 90 loop : -1.35 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.008 0.001 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 263) hydrogen bonds : angle 4.41821 ( 786) SS BOND : bond 0.00330 ( 4) SS BOND : angle 1.01064 ( 8) covalent geometry : bond 0.00321 ( 4740) covalent geometry : angle 0.58593 ( 6440) Misc. bond : bond 0.00028 ( 1) *********************** 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 138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 189 ILE cc_start: 0.8289 (mt) cc_final: 0.8019 (mt) REVERT: A 271 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: A 333 THR cc_start: 0.9132 (m) cc_final: 0.8829 (m) REVERT: A 384 TYR cc_start: 0.9035 (t80) cc_final: 0.8672 (t80) REVERT: H 49 GLU cc_start: 0.8435 (tt0) cc_final: 0.8171 (tt0) REVERT: H 68 LYS cc_start: 0.8426 (tttt) cc_final: 0.7987 (ttpp) REVERT: H 80 ASN cc_start: 0.8475 (t0) cc_final: 0.8202 (t0) REVERT: L 18 ASP cc_start: 0.8224 (m-30) cc_final: 0.7935 (m-30) REVERT: L 56 TYR cc_start: 0.8975 (t80) cc_final: 0.8635 (t80) REVERT: L 91 GLN cc_start: 0.9220 (pp30) cc_final: 0.8397 (pp30) outliers start: 26 outliers final: 23 residues processed: 127 average time/residue: 0.1785 time to fit residues: 28.7278 Evaluate side-chains 133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 7 GLN Chi-restraints excluded: chain L residue 10 SER 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: 0.6980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.121691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113390 restraints weight = 7875.700| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.98 r_work: 0.3287 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4745 Z= 0.137 Angle : 0.596 10.123 6448 Z= 0.304 Chirality : 0.042 0.153 739 Planarity : 0.004 0.047 788 Dihedral : 6.624 56.103 705 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.96 % Allowed : 21.63 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.35), residues: 574 helix: 1.37 (0.32), residues: 273 sheet: -0.45 (0.58), residues: 90 loop : -1.30 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.017 0.001 PHE A 268 TYR 0.012 0.001 TYR A 345 ARG 0.005 0.000 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 263) hydrogen bonds : angle 4.41190 ( 786) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.03659 ( 8) covalent geometry : bond 0.00305 ( 4740) covalent geometry : angle 0.59510 ( 6440) Misc. bond : bond 0.00028 ( 1) *********************** 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 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 189 ILE cc_start: 0.8276 (mt) cc_final: 0.8005 (mt) REVERT: A 271 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: A 305 MET cc_start: 0.8826 (mmm) cc_final: 0.8601 (mtp) REVERT: A 333 THR cc_start: 0.9130 (m) cc_final: 0.8830 (m) REVERT: A 384 TYR cc_start: 0.9043 (t80) cc_final: 0.8733 (t80) REVERT: H 49 GLU cc_start: 0.8401 (tt0) cc_final: 0.8145 (tt0) REVERT: H 68 LYS cc_start: 0.8418 (tttt) cc_final: 0.7973 (ttpp) REVERT: H 80 ASN cc_start: 0.8487 (t0) cc_final: 0.8225 (t0) REVERT: L 18 ASP cc_start: 0.8243 (m-30) cc_final: 0.7950 (m-30) REVERT: L 56 TYR cc_start: 0.8978 (t80) cc_final: 0.8643 (t80) REVERT: L 91 GLN cc_start: 0.9223 (pp30) cc_final: 0.8423 (pp30) outliers start: 25 outliers final: 22 residues processed: 126 average time/residue: 0.1735 time to fit residues: 27.6741 Evaluate side-chains 131 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 152 THR 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 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 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 3 ILE Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER 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: 0.0870 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 52 optimal weight: 0.1980 chunk 7 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115494 restraints weight = 7780.470| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.97 r_work: 0.3319 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4745 Z= 0.122 Angle : 0.567 6.713 6448 Z= 0.294 Chirality : 0.041 0.143 739 Planarity : 0.004 0.047 788 Dihedral : 6.526 56.959 705 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.16 % Allowed : 21.83 % Favored : 73.02 % 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: 0.25 (0.35), residues: 574 helix: 1.39 (0.32), residues: 275 sheet: -0.35 (0.59), residues: 90 loop : -1.23 (0.40), residues: 209 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 0.016 0.001 PHE A 268 TYR 0.009 0.001 TYR A 345 ARG 0.005 0.000 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 263) hydrogen bonds : angle 4.36817 ( 786) SS BOND : bond 0.00347 ( 4) SS BOND : angle 1.02932 ( 8) covalent geometry : bond 0.00267 ( 4740) covalent geometry : angle 0.56656 ( 6440) Misc. bond : bond 0.00013 ( 1) ********************** 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 141 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7763 (t80) cc_final: 0.6817 (m-80) REVERT: A 174 ILE cc_start: 0.9074 (mt) cc_final: 0.8839 (mm) REVERT: A 229 MET cc_start: 0.8221 (ptp) cc_final: 0.7867 (ptp) REVERT: A 271 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: A 294 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7782 (mtt90) REVERT: A 305 MET cc_start: 0.8753 (mmm) cc_final: 0.8396 (mtp) REVERT: A 333 THR cc_start: 0.9116 (m) cc_final: 0.8818 (m) REVERT: A 384 TYR cc_start: 0.9023 (t80) cc_final: 0.8666 (t80) REVERT: H 49 GLU cc_start: 0.8343 (tt0) cc_final: 0.8094 (tt0) REVERT: H 68 LYS cc_start: 0.8385 (tttt) cc_final: 0.7952 (ttpp) REVERT: H 80 ASN cc_start: 0.8487 (t0) cc_final: 0.8163 (t0) REVERT: L 18 ASP cc_start: 0.8174 (m-30) cc_final: 0.7911 (m-30) REVERT: L 56 TYR cc_start: 0.8940 (t80) cc_final: 0.8603 (t80) REVERT: L 73 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8611 (p) REVERT: L 91 GLN cc_start: 0.9200 (pp30) cc_final: 0.8338 (pp30) outliers start: 26 outliers final: 23 residues processed: 134 average time/residue: 0.3688 time to fit residues: 62.7582 Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 152 THR Chi-restraints excluded: chain A residue 154 ASN 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 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 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 3 ILE Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER 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: 0.6980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 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 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112102 restraints weight = 7878.405| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.97 r_work: 0.3269 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4745 Z= 0.150 Angle : 0.604 7.446 6448 Z= 0.311 Chirality : 0.043 0.186 739 Planarity : 0.004 0.044 788 Dihedral : 6.607 57.862 705 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.36 % Allowed : 22.42 % Favored : 72.22 % 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: 0.22 (0.35), residues: 574 helix: 1.40 (0.32), residues: 272 sheet: -0.33 (0.59), residues: 90 loop : -1.27 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 122 HIS 0.003 0.001 HIS H 38 PHE 0.018 0.001 PHE A 364 TYR 0.016 0.001 TYR A 345 ARG 0.008 0.001 ARG H 111 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 263) hydrogen bonds : angle 4.42566 ( 786) SS BOND : bond 0.00327 ( 4) SS BOND : angle 1.03422 ( 8) covalent geometry : bond 0.00338 ( 4740) covalent geometry : angle 0.60348 ( 6440) Misc. bond : bond 0.00037 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.70 seconds wall clock time: 56 minutes 35.96 seconds (3395.96 seconds total)