Starting phenix.real_space_refine on Sun Mar 10 19:57:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukj_20806/03_2024/6ukj_20806_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukj_20806/03_2024/6ukj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukj_20806/03_2024/6ukj_20806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukj_20806/03_2024/6ukj_20806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukj_20806/03_2024/6ukj_20806_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukj_20806/03_2024/6ukj_20806_neut.pdb" } 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 Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.09, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 1.77 Conformation dependent library (CDL) restraints added in 851.1 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: 0.47 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: 1.25 Time building geometry restraints manager: 1.93 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: 98.10 - 105.28: 67 105.28 - 112.47: 2349 112.47 - 119.66: 1622 119.66 - 126.84: 2360 126.84 - 134.03: 42 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 2.440 nonbonded pdb=" OG SER A 72 " pdb=" OE1 GLN A 352 " model vdw 2.216 2.440 nonbonded pdb=" OG SER A 157 " pdb=" OE2 GLU A 198 " model vdw 2.260 2.440 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 2.520 ... (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 ========== 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: 1.640 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: 5.980 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.910 Find NCS groups from input model: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 4740 Z= 0.456 Angle : 0.907 9.621 6440 Z= 0.477 Chirality : 0.052 0.381 739 Planarity : 0.005 0.047 788 Dihedral : 13.739 83.312 1708 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % Rotamer: Outliers : 0.79 % Allowed : 5.95 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.28), residues: 574 helix: -1.69 (0.25), residues: 263 sheet: -1.94 (0.47), residues: 93 loop : -2.58 (0.34), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 95 HIS 0.006 0.001 HIS H 38 PHE 0.018 0.002 PHE A 251 TYR 0.019 0.002 TYR H 102 ARG 0.013 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.511 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: 0.2135 time to fit residues: 33.1177 Evaluate side-chains 103 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain L residue 10 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4740 Z= 0.196 Angle : 0.580 7.170 6440 Z= 0.305 Chirality : 0.042 0.163 739 Planarity : 0.004 0.043 788 Dihedral : 7.782 56.962 710 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.78 % Allowed : 11.31 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.54 (0.32), residues: 574 helix: -0.06 (0.30), residues: 266 sheet: -1.16 (0.51), residues: 91 loop : -2.11 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 95 HIS 0.002 0.001 HIS A 180 PHE 0.015 0.001 PHE A 268 TYR 0.014 0.001 TYR A 345 ARG 0.006 0.001 ARG A 294 *********************** 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 137 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8451 (ptmt) cc_final: 0.8217 (ttpp) REVERT: A 106 PHE cc_start: 0.7456 (t80) cc_final: 0.6630 (m-10) REVERT: A 333 THR cc_start: 0.8775 (m) cc_final: 0.8507 (m) REVERT: A 347 ILE cc_start: 0.8190 (mm) cc_final: 0.7875 (mt) REVERT: A 384 TYR cc_start: 0.8524 (t80) cc_final: 0.8065 (t80) REVERT: H 68 LYS cc_start: 0.8304 (tttt) cc_final: 0.7919 (ttpp) REVERT: H 80 ASN cc_start: 0.8469 (t0) cc_final: 0.8159 (t0) REVERT: L 56 TYR cc_start: 0.8630 (t80) cc_final: 0.8182 (t80) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 0.1813 time to fit residues: 29.4658 Evaluate side-chains 114 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4740 Z= 0.190 Angle : 0.548 7.366 6440 Z= 0.287 Chirality : 0.042 0.143 739 Planarity : 0.004 0.041 788 Dihedral : 6.998 59.944 705 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.17 % Allowed : 13.89 % Favored : 81.94 % 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: -0.82 (0.34), residues: 574 helix: 0.59 (0.31), residues: 269 sheet: -0.80 (0.54), residues: 91 loop : -1.85 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 95 HIS 0.002 0.001 HIS H 38 PHE 0.014 0.001 PHE A 251 TYR 0.012 0.001 TYR A 345 ARG 0.004 0.000 ARG A 294 *********************** 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 139 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8933 (m) cc_final: 0.8608 (m) REVERT: A 347 ILE cc_start: 0.8100 (mm) cc_final: 0.7827 (mt) REVERT: A 384 TYR cc_start: 0.8519 (t80) cc_final: 0.8018 (t80) REVERT: H 68 LYS cc_start: 0.8306 (tttt) cc_final: 0.7965 (ttpp) REVERT: H 80 ASN cc_start: 0.8400 (t0) cc_final: 0.8088 (t0) REVERT: L 18 ASP cc_start: 0.7861 (m-30) cc_final: 0.7463 (m-30) REVERT: L 56 TYR cc_start: 0.8640 (t80) cc_final: 0.8372 (t80) outliers start: 21 outliers final: 18 residues processed: 132 average time/residue: 0.1866 time to fit residues: 30.4487 Evaluate side-chains 124 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4740 Z= 0.176 Angle : 0.552 7.586 6440 Z= 0.288 Chirality : 0.041 0.138 739 Planarity : 0.004 0.041 788 Dihedral : 6.847 59.956 705 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.96 % Allowed : 15.28 % Favored : 79.76 % 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: -0.34 (0.35), residues: 574 helix: 1.02 (0.32), residues: 269 sheet: -0.65 (0.56), residues: 91 loop : -1.62 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.001 0.000 HIS A 180 PHE 0.021 0.001 PHE A 268 TYR 0.011 0.001 TYR A 345 ARG 0.006 0.000 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8909 (m) cc_final: 0.8550 (m) REVERT: H 68 LYS cc_start: 0.8298 (tttt) cc_final: 0.7949 (ttpp) REVERT: H 80 ASN cc_start: 0.8303 (t0) cc_final: 0.8004 (t0) REVERT: L 18 ASP cc_start: 0.7805 (m-30) cc_final: 0.7356 (m-30) REVERT: L 56 TYR cc_start: 0.8640 (t80) cc_final: 0.8431 (t80) REVERT: L 73 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8391 (p) outliers start: 25 outliers final: 20 residues processed: 127 average time/residue: 0.1790 time to fit residues: 28.3878 Evaluate side-chains 128 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4740 Z= 0.182 Angle : 0.573 11.811 6440 Z= 0.290 Chirality : 0.041 0.137 739 Planarity : 0.004 0.040 788 Dihedral : 6.718 59.605 705 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.16 % Allowed : 16.87 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.35), residues: 574 helix: 1.24 (0.32), residues: 270 sheet: -0.42 (0.57), residues: 90 loop : -1.54 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.001 0.000 HIS A 180 PHE 0.016 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.006 0.000 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8089 (mm-30) REVERT: A 333 THR cc_start: 0.8923 (m) cc_final: 0.8569 (m) REVERT: H 68 LYS cc_start: 0.8287 (tttt) cc_final: 0.7928 (ttpp) REVERT: H 76 ASP cc_start: 0.7768 (m-30) cc_final: 0.7561 (m-30) REVERT: H 80 ASN cc_start: 0.8302 (t0) cc_final: 0.7980 (t0) REVERT: L 7 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: L 56 TYR cc_start: 0.8658 (t80) cc_final: 0.8372 (t80) outliers start: 26 outliers final: 22 residues processed: 130 average time/residue: 0.1766 time to fit residues: 28.7183 Evaluate side-chains 126 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 220 SER 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 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4740 Z= 0.183 Angle : 0.571 10.811 6440 Z= 0.290 Chirality : 0.041 0.133 739 Planarity : 0.004 0.041 788 Dihedral : 6.629 58.489 705 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.56 % Allowed : 17.06 % 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: 0.07 (0.36), residues: 574 helix: 1.34 (0.32), residues: 270 sheet: -0.35 (0.57), residues: 90 loop : -1.46 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.001 0.000 HIS A 180 PHE 0.017 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.007 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8931 (m) cc_final: 0.8566 (m) REVERT: H 68 LYS cc_start: 0.8295 (tttt) cc_final: 0.7932 (ttpp) REVERT: H 80 ASN cc_start: 0.8292 (t0) cc_final: 0.8004 (t0) REVERT: L 7 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: L 18 ASP cc_start: 0.7496 (m-30) cc_final: 0.7176 (m-30) outliers start: 28 outliers final: 24 residues processed: 130 average time/residue: 0.1733 time to fit residues: 28.1745 Evaluate side-chains 130 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 220 SER 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 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4740 Z= 0.190 Angle : 0.566 8.948 6440 Z= 0.292 Chirality : 0.041 0.135 739 Planarity : 0.004 0.041 788 Dihedral : 6.593 58.119 705 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.95 % Allowed : 18.25 % Favored : 75.79 % 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: 0.21 (0.36), residues: 574 helix: 1.44 (0.32), residues: 270 sheet: -0.30 (0.57), residues: 90 loop : -1.35 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.002 0.001 HIS A 180 PHE 0.016 0.001 PHE A 268 TYR 0.012 0.001 TYR A 345 ARG 0.006 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8938 (m) cc_final: 0.8583 (m) REVERT: H 68 LYS cc_start: 0.8293 (tttt) cc_final: 0.7929 (ttpp) REVERT: H 80 ASN cc_start: 0.8275 (t0) cc_final: 0.7999 (t0) REVERT: L 3 ILE cc_start: 0.8389 (mt) cc_final: 0.7649 (mt) REVERT: L 7 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7860 (tt0) outliers start: 30 outliers final: 26 residues processed: 128 average time/residue: 0.1681 time to fit residues: 27.0449 Evaluate side-chains 132 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4740 Z= 0.214 Angle : 0.580 7.075 6440 Z= 0.300 Chirality : 0.042 0.144 739 Planarity : 0.004 0.043 788 Dihedral : 6.655 58.181 705 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 6.35 % Allowed : 19.25 % Favored : 74.40 % 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: 0.24 (0.36), residues: 574 helix: 1.43 (0.32), residues: 270 sheet: -0.28 (0.57), residues: 90 loop : -1.29 (0.41), residues: 214 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 0.015 0.001 PHE A 268 TYR 0.014 0.001 TYR A 345 ARG 0.007 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLN cc_start: 0.7884 (tt0) cc_final: 0.7660 (tt0) REVERT: A 333 THR cc_start: 0.8946 (m) cc_final: 0.8590 (m) REVERT: H 68 LYS cc_start: 0.8328 (tttt) cc_final: 0.7956 (ttpp) REVERT: H 80 ASN cc_start: 0.8346 (t0) cc_final: 0.8079 (t0) REVERT: L 7 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: L 18 ASP cc_start: 0.7596 (m-30) cc_final: 0.7239 (m-30) outliers start: 32 outliers final: 28 residues processed: 128 average time/residue: 0.1683 time to fit residues: 27.0787 Evaluate side-chains 134 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 220 SER 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 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4740 Z= 0.201 Angle : 0.584 10.054 6440 Z= 0.297 Chirality : 0.041 0.137 739 Planarity : 0.004 0.043 788 Dihedral : 6.582 58.696 705 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.95 % Allowed : 19.44 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.36), residues: 574 helix: 1.47 (0.32), residues: 270 sheet: -0.24 (0.57), residues: 90 loop : -1.24 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.001 0.001 HIS A 180 PHE 0.016 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.007 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLN cc_start: 0.7848 (tt0) cc_final: 0.7636 (tt0) REVERT: A 333 THR cc_start: 0.8937 (m) cc_final: 0.8585 (m) REVERT: H 68 LYS cc_start: 0.8315 (tttt) cc_final: 0.7946 (ttpp) REVERT: H 80 ASN cc_start: 0.8306 (t0) cc_final: 0.8061 (t0) REVERT: L 7 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: L 18 ASP cc_start: 0.7581 (m-30) cc_final: 0.7187 (m-30) REVERT: L 91 GLN cc_start: 0.8787 (pp30) cc_final: 0.7711 (pp30) outliers start: 30 outliers final: 29 residues processed: 129 average time/residue: 0.1766 time to fit residues: 28.5011 Evaluate side-chains 134 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 100 ILE 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 220 SER 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 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4740 Z= 0.199 Angle : 0.567 6.861 6440 Z= 0.294 Chirality : 0.041 0.137 739 Planarity : 0.004 0.044 788 Dihedral : 6.558 58.781 705 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 6.15 % Allowed : 19.25 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.36), residues: 574 helix: 1.51 (0.32), residues: 270 sheet: -0.22 (0.57), residues: 90 loop : -1.23 (0.41), residues: 214 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 0.016 0.001 PHE A 268 TYR 0.013 0.001 TYR A 345 ARG 0.007 0.000 ARG H 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLN cc_start: 0.7836 (tt0) cc_final: 0.7626 (tt0) REVERT: A 333 THR cc_start: 0.8939 (m) cc_final: 0.8584 (m) REVERT: H 68 LYS cc_start: 0.8319 (tttt) cc_final: 0.7947 (ttpp) REVERT: H 80 ASN cc_start: 0.8303 (t0) cc_final: 0.8003 (t0) REVERT: L 7 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: L 18 ASP cc_start: 0.7567 (m-30) cc_final: 0.7169 (m-30) REVERT: L 91 GLN cc_start: 0.8786 (pp30) cc_final: 0.7726 (pp30) outliers start: 31 outliers final: 29 residues processed: 128 average time/residue: 0.1711 time to fit residues: 27.4104 Evaluate side-chains 135 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 100 ILE 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 220 SER Chi-restraints excluded: chain A residue 258 CYS 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 6 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109456 restraints weight = 7862.771| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.02 r_work: 0.3219 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4740 Z= 0.189 Angle : 0.572 10.192 6440 Z= 0.292 Chirality : 0.041 0.131 739 Planarity : 0.004 0.044 788 Dihedral : 6.489 58.362 705 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.75 % Allowed : 20.24 % 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: 0.41 (0.36), residues: 574 helix: 1.56 (0.32), residues: 270 sheet: -0.15 (0.57), residues: 90 loop : -1.21 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 95 HIS 0.001 0.000 HIS H 38 PHE 0.016 0.001 PHE A 268 TYR 0.014 0.001 TYR A 345 ARG 0.007 0.001 ARG H 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.87 seconds wall clock time: 27 minutes 55.86 seconds (1675.86 seconds total)