Starting phenix.real_space_refine on Wed Mar 5 15:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j28_35947/03_2025/8j28_35947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j28_35947/03_2025/8j28_35947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j28_35947/03_2025/8j28_35947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j28_35947/03_2025/8j28_35947.map" model { file = "/net/cci-nas-00/data/ceres_data/8j28_35947/03_2025/8j28_35947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j28_35947/03_2025/8j28_35947.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 9 5.16 5 C 1572 2.51 5 N 441 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 2499 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 147 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "C" Number of atoms: 2047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2048 Chain: "E" Number of atoms: 140 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Conformer: "B" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} bond proxies already assigned to first conformer: 115 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR C 72 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 72 " occ=0.50 residue: pdb=" N ATYR E 72 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 72 " occ=0.50 Time building chain proxies: 3.59, per 1000 atoms: 1.44 Number of scatterers: 2499 At special positions: 0 Unit cell: (74.2, 68.9, 78.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 3 15.00 O 474 8.00 N 441 7.00 C 1572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 556.9 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " Number of C-beta restraints generated: 584 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 56.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.624A pdb=" N LYS C 12 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.601A pdb=" N GLY C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 91 through 114 removed outlier: 4.226A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.898A pdb=" N PHE C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.813A pdb=" N LYS C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 238 through 251 removed outlier: 4.193A pdb=" N LYS C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 123 removed outlier: 3.670A pdb=" N ALA C 119 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 152 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 121 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C 154 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 123 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL C 55 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE C 153 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 57 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLU C 155 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER C 59 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 191 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 257 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 256 " --> pdb=" O PHE C 280 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 409 1.31 - 1.44: 662 1.44 - 1.56: 1444 1.56 - 1.69: 4 1.69 - 1.82: 16 Bond restraints: 2535 Sorted by residual: bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.648 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD RGP C 802 " pdb=" OE2 RGP C 802 " ideal model delta sigma weight residual 1.302 1.397 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" N ARG C 67 " pdb=" CA ARG C 67 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA LEU C 65 " pdb=" C LEU C 65 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.36e-02 5.41e+03 8.67e+00 bond pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.39e-02 5.18e+03 6.34e+00 ... (remaining 2530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 3315 2.36 - 4.72: 81 4.72 - 7.09: 17 7.09 - 9.45: 5 9.45 - 11.81: 1 Bond angle restraints: 3419 Sorted by residual: angle pdb=" N LEU C 65 " pdb=" CA LEU C 65 " pdb=" C LEU C 65 " ideal model delta sigma weight residual 111.71 103.48 8.23 1.15e+00 7.56e-01 5.12e+01 angle pdb=" N LEU E 83 " pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 111.75 103.06 8.69 1.28e+00 6.10e-01 4.61e+01 angle pdb=" N VAL C 25 " pdb=" CA VAL C 25 " pdb=" C VAL C 25 " ideal model delta sigma weight residual 113.42 108.56 4.86 1.17e+00 7.31e-01 1.72e+01 angle pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " pdb=" OA3 RGP C 802 " ideal model delta sigma weight residual 97.78 109.59 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N ARG C 67 " pdb=" CA ARG C 67 " pdb=" C ARG C 67 " ideal model delta sigma weight residual 111.11 106.67 4.44 1.20e+00 6.94e-01 1.37e+01 ... (remaining 3414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.27: 1458 33.27 - 66.54: 60 66.54 - 99.80: 5 99.80 - 133.07: 1 133.07 - 166.33: 1 Dihedral angle restraints: 1525 sinusoidal: 618 harmonic: 907 Sorted by residual: dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 106.33 -166.33 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " pdb=" O2A ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 40.34 -100.34 1 2.00e+01 2.50e-03 2.83e+01 dihedral pdb=" CA GLU C 220 " pdb=" C GLU C 220 " pdb=" N LYS C 221 " pdb=" CA LYS C 221 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 231 0.031 - 0.061: 103 0.061 - 0.092: 29 0.092 - 0.122: 22 0.122 - 0.153: 5 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA GLN C 68 " pdb=" N GLN C 68 " pdb=" C GLN C 68 " pdb=" CB GLN C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE C 56 " pdb=" N ILE C 56 " pdb=" C ILE C 56 " pdb=" CB ILE C 56 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE C 150 " pdb=" N ILE C 150 " pdb=" C ILE C 150 " pdb=" CB ILE C 150 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 387 not shown) Planarity restraints: 431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTYR C 72 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C BTYR C 72 " 0.067 2.00e-02 2.50e+03 pdb=" O BTYR C 72 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG C 73 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 71 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG C 71 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG C 71 " 0.023 2.00e-02 2.50e+03 pdb=" N ATYR C 72 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATYR C 72 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ATYR C 72 " 0.062 2.00e-02 2.50e+03 pdb=" O ATYR C 72 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG C 73 " -0.021 2.00e-02 2.50e+03 ... (remaining 428 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 368 2.75 - 3.29: 2499 3.29 - 3.83: 3975 3.83 - 4.36: 4469 4.36 - 4.90: 7524 Nonbonded interactions: 18835 Sorted by model distance: nonbonded pdb=" OE2 GLU C 199 " pdb=" OH TYR C 202 " model vdw 2.213 3.040 nonbonded pdb=" OG SER C 60 " pdb=" OD1 ASN C 176 " model vdw 2.223 3.040 nonbonded pdb=" N GLU C 199 " pdb=" OE1 GLU C 199 " model vdw 2.252 3.120 nonbonded pdb=" O THR C 161 " pdb=" OG1 THR C 161 " model vdw 2.295 3.040 nonbonded pdb=" O SER F 79 " pdb=" N ASP F 82 " model vdw 2.345 3.120 ... (remaining 18830 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 71 or resid 73 through 85)) selection = (chain 'E' and (resid 71 or resid 73 through 85)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.720 Find NCS groups from input model: 0.040 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.006 0.150 2535 Z= 0.359 Angle : 0.923 11.812 3419 Z= 0.531 Chirality : 0.044 0.153 390 Planarity : 0.005 0.039 431 Dihedral : 17.631 166.335 941 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.28 % Allowed : 21.29 % Favored : 76.43 % 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: -1.56 (0.46), residues: 307 helix: -0.70 (0.38), residues: 166 sheet: -0.37 (0.84), residues: 42 loop : -1.65 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 287 HIS 0.005 0.001 HIS C 222 PHE 0.015 0.001 PHE C 128 TYR 0.007 0.001 TYR A 72 ARG 0.003 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: F 75 LEU cc_start: 0.9313 (mm) cc_final: 0.9106 (mp) REVERT: F 82 ASP cc_start: 0.9501 (m-30) cc_final: 0.9277 (m-30) REVERT: A 73 ARG cc_start: 0.9110 (tpt90) cc_final: 0.8073 (ttp-170) REVERT: C 47 GLU cc_start: 0.8001 (pp20) cc_final: 0.7759 (pp20) REVERT: C 73 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8136 (tmt170) REVERT: C 100 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 154 ASN cc_start: 0.8312 (t0) cc_final: 0.8109 (t0) REVERT: C 198 VAL cc_start: 0.8813 (m) cc_final: 0.8598 (p) REVERT: C 208 ASP cc_start: 0.7813 (p0) cc_final: 0.7602 (p0) outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 0.2078 time to fit residues: 28.2316 Evaluate side-chains 87 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098708 restraints weight = 33125.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103715 restraints weight = 8260.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107099 restraints weight = 4010.140| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2535 Z= 0.205 Angle : 0.715 6.155 3419 Z= 0.352 Chirality : 0.041 0.147 390 Planarity : 0.005 0.043 431 Dihedral : 12.155 148.394 367 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.42 % Allowed : 31.18 % Favored : 65.40 % 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: -0.39 (0.48), residues: 307 helix: 0.53 (0.40), residues: 166 sheet: -0.38 (0.81), residues: 46 loop : -1.47 (0.63), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.008 0.002 HIS C 222 PHE 0.019 0.002 PHE F 80 TYR 0.014 0.002 TYR F 72 ARG 0.009 0.001 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8859 (tpt90) cc_final: 0.7923 (ttt180) REVERT: C 47 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8813 (pp20) REVERT: C 73 ARG cc_start: 0.8763 (mmm160) cc_final: 0.7753 (tmt170) REVERT: C 100 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8210 (tm-30) REVERT: C 154 ASN cc_start: 0.8697 (t0) cc_final: 0.8394 (t0) REVERT: C 198 VAL cc_start: 0.9312 (m) cc_final: 0.9103 (p) REVERT: C 199 GLU cc_start: 0.9000 (pm20) cc_final: 0.8699 (pm20) REVERT: C 223 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 239 MET cc_start: 0.8306 (mtp) cc_final: 0.8060 (mtp) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.1996 time to fit residues: 22.5635 Evaluate side-chains 93 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.0070 chunk 28 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN C 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098096 restraints weight = 33075.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103145 restraints weight = 8721.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106496 restraints weight = 4276.592| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2535 Z= 0.184 Angle : 0.724 8.751 3419 Z= 0.342 Chirality : 0.043 0.139 390 Planarity : 0.004 0.032 431 Dihedral : 11.015 128.310 365 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.84 % Allowed : 28.14 % Favored : 65.02 % 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: -0.30 (0.48), residues: 307 helix: 0.55 (0.40), residues: 166 sheet: -0.37 (0.81), residues: 46 loop : -1.29 (0.64), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 PHE 0.026 0.002 PHE F 80 TYR 0.003 0.001 TYR C 202 ARG 0.007 0.001 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8873 (tpt90) cc_final: 0.7907 (ttp-170) REVERT: C 47 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8827 (pp20) REVERT: C 73 ARG cc_start: 0.8869 (mmm160) cc_final: 0.7686 (tmt170) REVERT: C 88 MET cc_start: 0.8194 (mmp) cc_final: 0.7942 (tpp) REVERT: C 100 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 154 ASN cc_start: 0.8690 (t0) cc_final: 0.8381 (t0) REVERT: C 198 VAL cc_start: 0.9345 (m) cc_final: 0.9130 (p) REVERT: C 199 GLU cc_start: 0.8992 (pm20) cc_final: 0.8753 (pm20) REVERT: C 219 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8984 (mmtp) REVERT: C 239 MET cc_start: 0.8430 (mtp) cc_final: 0.8145 (mtp) REVERT: E 71 ARG cc_start: 0.7118 (mpp-170) cc_final: 0.6561 (mpp-170) REVERT: E 73 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7504 (tmt170) outliers start: 18 outliers final: 7 residues processed: 100 average time/residue: 0.2026 time to fit residues: 22.9540 Evaluate side-chains 99 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain E residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097629 restraints weight = 32670.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102582 restraints weight = 8295.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105955 restraints weight = 4053.043| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2535 Z= 0.188 Angle : 0.718 9.688 3419 Z= 0.340 Chirality : 0.044 0.263 390 Planarity : 0.004 0.027 431 Dihedral : 10.418 106.540 365 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.46 % Allowed : 30.04 % Favored : 63.50 % 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 (0.49), residues: 307 helix: 0.67 (0.41), residues: 166 sheet: -0.47 (0.80), residues: 46 loop : -1.15 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.028 0.003 PHE C 80 TYR 0.002 0.001 TYR C 202 ARG 0.005 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8888 (tpt90) cc_final: 0.7894 (ttp-170) REVERT: C 12 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8336 (mttt) REVERT: C 47 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8856 (pp20) REVERT: C 73 ARG cc_start: 0.8862 (mmm160) cc_final: 0.7620 (tmt170) REVERT: C 93 LYS cc_start: 0.8229 (mttt) cc_final: 0.7443 (pttt) REVERT: C 100 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 154 ASN cc_start: 0.8734 (t0) cc_final: 0.8415 (t0) REVERT: C 198 VAL cc_start: 0.9362 (m) cc_final: 0.9148 (p) REVERT: C 199 GLU cc_start: 0.9033 (pm20) cc_final: 0.8794 (pm20) REVERT: C 239 MET cc_start: 0.8535 (mtp) cc_final: 0.8121 (mtp) REVERT: E 71 ARG cc_start: 0.6896 (mpp-170) cc_final: 0.6414 (mpp-170) REVERT: E 73 ARG cc_start: 0.8014 (ptp90) cc_final: 0.7439 (tmt170) REVERT: E 77 ASN cc_start: 0.9453 (OUTLIER) cc_final: 0.8865 (m110) outliers start: 17 outliers final: 6 residues processed: 95 average time/residue: 0.2083 time to fit residues: 22.3945 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain E residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096968 restraints weight = 37884.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102004 restraints weight = 8732.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105480 restraints weight = 4169.455| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2535 Z= 0.196 Angle : 0.743 9.980 3419 Z= 0.350 Chirality : 0.044 0.243 390 Planarity : 0.003 0.027 431 Dihedral : 9.988 98.944 365 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.94 % Allowed : 31.94 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.50), residues: 307 helix: 0.59 (0.41), residues: 166 sheet: -0.36 (0.80), residues: 51 loop : -1.15 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.014 0.002 PHE A 80 TYR 0.002 0.000 TYR A 72 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8899 (tpt90) cc_final: 0.7866 (ttt180) REVERT: C 12 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8367 (mttt) REVERT: C 47 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8847 (pp20) REVERT: C 73 ARG cc_start: 0.8875 (mmm160) cc_final: 0.7613 (tmt170) REVERT: C 93 LYS cc_start: 0.8204 (mttt) cc_final: 0.7410 (pttt) REVERT: C 100 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 154 ASN cc_start: 0.8721 (t0) cc_final: 0.8403 (t0) REVERT: C 198 VAL cc_start: 0.9365 (m) cc_final: 0.9142 (p) REVERT: C 199 GLU cc_start: 0.9016 (pm20) cc_final: 0.8811 (pm20) REVERT: C 239 MET cc_start: 0.8619 (mtp) cc_final: 0.8218 (mtp) REVERT: E 71 ARG cc_start: 0.6944 (mpp-170) cc_final: 0.6542 (mpp-170) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.1954 time to fit residues: 21.1959 Evaluate side-chains 93 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN C 248 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094572 restraints weight = 34330.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099484 restraints weight = 8721.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102808 restraints weight = 4259.985| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2535 Z= 0.253 Angle : 0.734 6.527 3419 Z= 0.352 Chirality : 0.044 0.183 390 Planarity : 0.004 0.024 431 Dihedral : 9.644 94.447 365 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.70 % Allowed : 31.56 % Favored : 62.74 % 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 (0.49), residues: 307 helix: 0.68 (0.41), residues: 166 sheet: -0.12 (1.00), residues: 30 loop : -1.27 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.007 0.002 HIS C 222 PHE 0.030 0.002 PHE F 80 TYR 0.005 0.001 TYR C 251 ARG 0.004 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8971 (tpt90) cc_final: 0.7977 (ttt180) REVERT: C 12 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8403 (mttt) REVERT: C 42 CYS cc_start: 0.9013 (m) cc_final: 0.8540 (t) REVERT: C 47 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8871 (pp20) REVERT: C 73 ARG cc_start: 0.8896 (mmm160) cc_final: 0.7563 (tmt170) REVERT: C 93 LYS cc_start: 0.8365 (mttt) cc_final: 0.7623 (pttt) REVERT: C 100 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 154 ASN cc_start: 0.8795 (t0) cc_final: 0.8447 (t0) REVERT: C 198 VAL cc_start: 0.9424 (m) cc_final: 0.9173 (p) REVERT: C 199 GLU cc_start: 0.9037 (pm20) cc_final: 0.8787 (pm20) REVERT: C 239 MET cc_start: 0.8718 (mtp) cc_final: 0.8303 (mtp) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 0.1927 time to fit residues: 20.1196 Evaluate side-chains 91 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096386 restraints weight = 28410.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101196 restraints weight = 8002.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104458 restraints weight = 4003.889| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2535 Z= 0.237 Angle : 0.771 8.832 3419 Z= 0.362 Chirality : 0.044 0.138 390 Planarity : 0.003 0.027 431 Dihedral : 9.493 90.560 365 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.56 % Allowed : 34.22 % Favored : 61.22 % 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: -0.20 (0.48), residues: 307 helix: 0.65 (0.40), residues: 166 sheet: -0.24 (0.95), residues: 30 loop : -1.23 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.004 0.001 HIS C 222 PHE 0.033 0.002 PHE F 80 TYR 0.002 0.001 TYR C 251 ARG 0.003 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.285 Fit side-chains REVERT: A 73 ARG cc_start: 0.8971 (tpt90) cc_final: 0.7966 (ttt180) REVERT: C 12 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8381 (mttt) REVERT: C 42 CYS cc_start: 0.8974 (m) cc_final: 0.8474 (t) REVERT: C 47 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8866 (pp20) REVERT: C 93 LYS cc_start: 0.8350 (mttt) cc_final: 0.7545 (pttt) REVERT: C 100 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 154 ASN cc_start: 0.8784 (t0) cc_final: 0.8442 (t0) REVERT: C 198 VAL cc_start: 0.9436 (m) cc_final: 0.9192 (p) REVERT: C 199 GLU cc_start: 0.9042 (pm20) cc_final: 0.8809 (pm20) REVERT: C 239 MET cc_start: 0.8700 (mtp) cc_final: 0.8275 (mtp) REVERT: C 275 ARG cc_start: 0.5454 (mmt180) cc_final: 0.4611 (ttm-80) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.1799 time to fit residues: 18.5742 Evaluate side-chains 87 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.122576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098091 restraints weight = 25438.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.102916 restraints weight = 7548.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106128 restraints weight = 3850.106| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2535 Z= 0.208 Angle : 0.785 8.838 3419 Z= 0.365 Chirality : 0.044 0.143 390 Planarity : 0.004 0.038 431 Dihedral : 9.426 86.357 365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.80 % Allowed : 36.88 % Favored : 59.32 % 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: -0.15 (0.48), residues: 307 helix: 0.66 (0.40), residues: 166 sheet: -0.32 (0.94), residues: 30 loop : -1.11 (0.61), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 174 HIS 0.007 0.001 HIS C 222 PHE 0.031 0.002 PHE F 80 TYR 0.015 0.001 TYR F 72 ARG 0.003 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.298 Fit side-chains REVERT: A 73 ARG cc_start: 0.8920 (tpt90) cc_final: 0.8017 (ttt180) REVERT: C 12 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8711 (mmtt) REVERT: C 17 ILE cc_start: 0.8371 (mt) cc_final: 0.7940 (tt) REVERT: C 47 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8855 (pp20) REVERT: C 93 LYS cc_start: 0.8294 (mttt) cc_final: 0.7499 (pttt) REVERT: C 100 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 154 ASN cc_start: 0.8751 (t0) cc_final: 0.8421 (t0) REVERT: C 198 VAL cc_start: 0.9397 (m) cc_final: 0.9150 (p) REVERT: C 199 GLU cc_start: 0.9082 (pm20) cc_final: 0.8864 (pm20) REVERT: C 239 MET cc_start: 0.8668 (mtp) cc_final: 0.8261 (mtp) REVERT: C 275 ARG cc_start: 0.5375 (mmt180) cc_final: 0.4553 (ttm-80) REVERT: E 84 GLN cc_start: 0.9271 (tp-100) cc_final: 0.9001 (mt0) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.1864 time to fit residues: 19.5210 Evaluate side-chains 93 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097324 restraints weight = 34246.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102514 restraints weight = 8456.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105939 restraints weight = 4086.082| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2535 Z= 0.222 Angle : 0.828 9.326 3419 Z= 0.388 Chirality : 0.045 0.173 390 Planarity : 0.003 0.031 431 Dihedral : 9.427 85.167 365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.18 % Allowed : 36.50 % Favored : 59.32 % 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: -0.35 (0.48), residues: 307 helix: 0.59 (0.41), residues: 166 sheet: -1.15 (0.87), residues: 35 loop : -1.09 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.004 0.001 HIS C 222 PHE 0.030 0.002 PHE F 80 TYR 0.031 0.002 TYR A 72 ARG 0.003 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8966 (tpt90) cc_final: 0.8017 (ttt180) REVERT: C 12 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8721 (mmtt) REVERT: C 17 ILE cc_start: 0.8452 (mt) cc_final: 0.8068 (tt) REVERT: C 47 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8860 (pp20) REVERT: C 93 LYS cc_start: 0.8288 (mttt) cc_final: 0.7492 (pttt) REVERT: C 100 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 154 ASN cc_start: 0.8707 (t0) cc_final: 0.8388 (t0) REVERT: C 198 VAL cc_start: 0.9461 (m) cc_final: 0.9205 (p) REVERT: C 239 MET cc_start: 0.8658 (mtp) cc_final: 0.8284 (mtp) REVERT: C 275 ARG cc_start: 0.5418 (mmt180) cc_final: 0.4579 (ttm-80) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.1844 time to fit residues: 18.9424 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 84 GLN C 248 ASN E 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098539 restraints weight = 30935.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.103717 restraints weight = 7992.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107082 restraints weight = 3866.770| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2535 Z= 0.206 Angle : 0.837 8.768 3419 Z= 0.388 Chirality : 0.045 0.162 390 Planarity : 0.004 0.028 431 Dihedral : 9.403 86.966 365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.56 % Allowed : 36.50 % Favored : 58.94 % 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: -0.50 (0.48), residues: 307 helix: 0.33 (0.40), residues: 172 sheet: -1.24 (0.87), residues: 35 loop : -0.94 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 PHE 0.033 0.002 PHE F 80 TYR 0.015 0.002 TYR F 72 ARG 0.003 0.000 ARG C 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8977 (tpt90) cc_final: 0.8027 (ttt180) REVERT: C 17 ILE cc_start: 0.8471 (mt) cc_final: 0.8059 (tt) REVERT: C 47 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8840 (pp20) REVERT: C 93 LYS cc_start: 0.8124 (mttt) cc_final: 0.7370 (pttt) REVERT: C 100 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8389 (tm-30) REVERT: C 154 ASN cc_start: 0.8703 (t0) cc_final: 0.8383 (t0) REVERT: C 239 MET cc_start: 0.8639 (mtp) cc_final: 0.8278 (mtp) REVERT: C 275 ARG cc_start: 0.5409 (mmt180) cc_final: 0.3803 (ttm170) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.1941 time to fit residues: 19.8752 Evaluate side-chains 93 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 84 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN E 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100305 restraints weight = 20278.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104958 restraints weight = 6591.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108002 restraints weight = 3398.935| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2535 Z= 0.211 Angle : 0.855 9.245 3419 Z= 0.404 Chirality : 0.046 0.191 390 Planarity : 0.003 0.029 431 Dihedral : 9.327 87.988 365 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.56 % Allowed : 36.88 % Favored : 58.56 % 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: -0.52 (0.48), residues: 307 helix: 0.33 (0.40), residues: 172 sheet: -1.26 (0.87), residues: 35 loop : -0.97 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.004 0.001 HIS C 222 PHE 0.028 0.002 PHE F 80 TYR 0.013 0.001 TYR C 251 ARG 0.003 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.51 seconds wall clock time: 26 minutes 42.62 seconds (1602.62 seconds total)