Starting phenix.real_space_refine on Thu Jul 18 21:32:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/07_2024/8sdz_40355.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/07_2024/8sdz_40355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/07_2024/8sdz_40355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/07_2024/8sdz_40355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/07_2024/8sdz_40355.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/07_2024/8sdz_40355.cif" } resolution = 2.86 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= 0.002 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 31 5.16 5 C 2533 2.51 5 N 654 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ASP 514": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3913 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 26, 'TRANS': 473} Chain breaks: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 41 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1, 'water': 22} Link IDs: {None: 22} Time building chain proxies: 3.00, per 1000 atoms: 0.77 Number of scatterers: 3913 At special positions: 0 Unit cell: (78.85, 71.38, 98.77, 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 31 16.00 O 695 8.00 N 654 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 846.3 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 80.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.963A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.115A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.569A pdb=" N SER A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 6.057A pdb=" N HIS A 217 " --> pdb=" O MET A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.585A pdb=" N VAL A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.711A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 355 removed outlier: 3.580A pdb=" N HIS A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 Processing helix chain 'A' and resid 419 through 449 Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix removed outlier: 3.880A pdb=" N ALA A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.834A pdb=" N LEU A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 272 hydrogen bonds defined for protein. 801 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: 1.21 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1217 1.35 - 1.46: 974 1.46 - 1.58: 1743 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 3983 Sorted by residual: bond pdb=" N04 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.625 1.712 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C11 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.776 1.820 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" CB PRO A 505 " pdb=" CG PRO A 505 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB MET A 23 " pdb=" CG MET A 23 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" O09 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.446 1.462 -0.016 2.00e-02 2.50e+03 6.14e-01 ... (remaining 3978 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.38: 158 107.38 - 114.04: 2270 114.04 - 120.69: 1799 120.69 - 127.35: 1142 127.35 - 134.01: 50 Bond angle restraints: 5419 Sorted by residual: angle pdb=" O09 RTO A 601 " pdb=" S08 RTO A 601 " pdb=" O10 RTO A 601 " ideal model delta sigma weight residual 119.19 101.11 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA MET A 23 " pdb=" CB MET A 23 " pdb=" CG MET A 23 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.29e+00 angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 108.88 113.75 -4.87 2.16e+00 2.14e-01 5.09e+00 ... (remaining 5414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2037 16.88 - 33.76: 237 33.76 - 50.64: 70 50.64 - 67.52: 18 67.52 - 84.40: 7 Dihedral angle restraints: 2369 sinusoidal: 926 harmonic: 1443 Sorted by residual: dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 2.02 -75.02 1 2.00e+01 2.50e-03 1.78e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -113.39 27.39 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" SG CYS A 49 " pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" CA CYS A 105 " ideal model delta sinusoidal sigma weight residual 79.00 24.03 54.97 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 2366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 487 0.039 - 0.077: 116 0.077 - 0.116: 22 0.116 - 0.154: 4 0.154 - 0.193: 2 Chirality restraints: 631 Sorted by residual: chirality pdb=" CG LEU A 6 " pdb=" CB LEU A 6 " pdb=" CD1 LEU A 6 " pdb=" CD2 LEU A 6 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CG LEU A 232 " pdb=" CB LEU A 232 " pdb=" CD1 LEU A 232 " pdb=" CD2 LEU A 232 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 628 not shown) Planarity restraints: 673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 213 " 0.014 2.00e-02 2.50e+03 1.38e-02 4.79e+00 pdb=" CG TRP A 213 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 213 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 213 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 213 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 213 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 26 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 27 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 256 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A 257 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.014 5.00e-02 4.00e+02 ... (remaining 670 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 67 2.69 - 3.24: 3898 3.24 - 3.79: 6341 3.79 - 4.35: 8704 4.35 - 4.90: 14135 Nonbonded interactions: 33145 Sorted by model distance: nonbonded pdb=" O VAL A 475 " pdb=" OG1 THR A 478 " model vdw 2.135 2.440 nonbonded pdb=" OG SER A 33 " pdb=" O HOH A 701 " model vdw 2.191 2.440 nonbonded pdb=" OD1 ASN A 168 " pdb=" OG SER A 201 " model vdw 2.211 2.440 nonbonded pdb=" O LEU A 29 " pdb=" O HOH A 701 " model vdw 2.216 2.440 nonbonded pdb=" O GLY A 233 " pdb=" O HOH A 701 " model vdw 2.234 2.440 ... (remaining 33140 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: 0.280 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.003 0.087 3983 Z= 0.164 Angle : 0.588 18.076 5419 Z= 0.261 Chirality : 0.036 0.193 631 Planarity : 0.003 0.028 673 Dihedral : 16.554 84.396 1435 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 20.24 % Favored : 78.33 % 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: 0.91 (0.37), residues: 492 helix: 0.73 (0.26), residues: 374 sheet: 0.04 (1.43), residues: 10 loop : 0.67 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 213 HIS 0.001 0.000 HIS A 48 PHE 0.007 0.001 PHE A 191 TYR 0.013 0.001 TYR A 264 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.436 Fit side-chains REVERT: A 280 ARG cc_start: 0.5134 (mmm160) cc_final: 0.4856 (tpp-160) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 1.0858 time to fit residues: 73.2548 Evaluate side-chains 60 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 38 GLN A 234 GLN A 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3983 Z= 0.166 Angle : 0.536 7.029 5419 Z= 0.265 Chirality : 0.038 0.164 631 Planarity : 0.004 0.029 673 Dihedral : 6.918 67.371 571 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.81 % Allowed : 18.81 % 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: 2.00 (0.38), residues: 492 helix: 1.52 (0.27), residues: 368 sheet: 0.64 (1.34), residues: 10 loop : 1.07 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 213 HIS 0.002 0.001 HIS A 249 PHE 0.019 0.001 PHE A 351 TYR 0.020 0.001 TYR A 264 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7584 (m-40) cc_final: 0.6924 (t0) outliers start: 16 outliers final: 6 residues processed: 67 average time/residue: 0.9320 time to fit residues: 65.2287 Evaluate side-chains 58 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3983 Z= 0.148 Angle : 0.471 6.234 5419 Z= 0.236 Chirality : 0.036 0.125 631 Planarity : 0.003 0.027 673 Dihedral : 6.510 63.685 566 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.81 % Allowed : 18.81 % 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: 2.23 (0.39), residues: 492 helix: 1.71 (0.27), residues: 368 sheet: 0.74 (1.29), residues: 10 loop : 1.08 (0.66), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 213 HIS 0.002 0.000 HIS A 337 PHE 0.016 0.001 PHE A 351 TYR 0.012 0.001 TYR A 264 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7534 (m-40) cc_final: 0.6926 (t0) REVERT: A 232 LEU cc_start: 0.8289 (mt) cc_final: 0.8085 (mm) REVERT: A 447 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7682 (mt-10) outliers start: 16 outliers final: 7 residues processed: 71 average time/residue: 0.9673 time to fit residues: 71.8424 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3983 Z= 0.223 Angle : 0.518 7.979 5419 Z= 0.258 Chirality : 0.038 0.124 631 Planarity : 0.003 0.027 673 Dihedral : 6.683 66.054 566 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.05 % Allowed : 18.33 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.38), residues: 492 helix: 1.68 (0.27), residues: 362 sheet: 0.19 (1.31), residues: 10 loop : 1.02 (0.63), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.001 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7549 (m-40) cc_final: 0.6860 (t0) REVERT: A 417 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7760 (mppt) REVERT: A 431 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7257 (tmtm) REVERT: A 447 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7630 (mt-10) outliers start: 17 outliers final: 11 residues processed: 68 average time/residue: 0.8715 time to fit residues: 62.0901 Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3983 Z= 0.207 Angle : 0.499 6.459 5419 Z= 0.250 Chirality : 0.038 0.125 631 Planarity : 0.003 0.027 673 Dihedral : 6.719 64.857 566 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.52 % Allowed : 17.14 % Favored : 78.33 % 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: 2.00 (0.38), residues: 492 helix: 1.61 (0.27), residues: 369 sheet: 0.10 (1.38), residues: 10 loop : 0.78 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7644 (m-40) cc_final: 0.7223 (t0) REVERT: A 212 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6616 (mt-10) REVERT: A 386 PHE cc_start: 0.6896 (m-10) cc_final: 0.6189 (t80) REVERT: A 417 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7763 (mppt) REVERT: A 431 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7247 (tmtm) REVERT: A 444 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 447 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7714 (mt-10) outliers start: 19 outliers final: 12 residues processed: 71 average time/residue: 0.8934 time to fit residues: 66.3331 Evaluate side-chains 68 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3983 Z= 0.143 Angle : 0.487 8.387 5419 Z= 0.238 Chirality : 0.036 0.138 631 Planarity : 0.003 0.026 673 Dihedral : 6.589 60.864 566 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.24 % Allowed : 17.14 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.39), residues: 492 helix: 1.78 (0.27), residues: 369 sheet: 0.02 (1.46), residues: 10 loop : 0.86 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.014 0.001 TYR A 264 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7679 (m-40) cc_final: 0.7264 (t0) REVERT: A 207 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5467 (tpt) REVERT: A 212 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6743 (mt-10) REVERT: A 386 PHE cc_start: 0.6890 (m-10) cc_final: 0.6185 (t80) outliers start: 22 outliers final: 12 residues processed: 74 average time/residue: 0.8372 time to fit residues: 64.9883 Evaluate side-chains 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3983 Z= 0.326 Angle : 0.569 6.949 5419 Z= 0.284 Chirality : 0.041 0.131 631 Planarity : 0.004 0.028 673 Dihedral : 7.158 69.918 566 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.05 % Allowed : 18.57 % 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: 1.76 (0.38), residues: 492 helix: 1.41 (0.27), residues: 369 sheet: -0.10 (1.64), residues: 10 loop : 0.76 (0.64), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.015 0.002 PHE A 191 TYR 0.022 0.002 TYR A 264 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7623 (m-40) cc_final: 0.7249 (t0) REVERT: A 207 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5447 (tpt) REVERT: A 212 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6832 (mt-10) REVERT: A 431 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7220 (tmtm) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.8533 time to fit residues: 60.8299 Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 0.0020 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3983 Z= 0.136 Angle : 0.484 6.672 5419 Z= 0.239 Chirality : 0.036 0.125 631 Planarity : 0.003 0.027 673 Dihedral : 6.742 61.215 566 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.81 % Allowed : 19.05 % Favored : 77.14 % 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: 2.15 (0.39), residues: 492 helix: 1.74 (0.27), residues: 369 sheet: -0.12 (1.63), residues: 10 loop : 0.75 (0.64), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 213 HIS 0.002 0.001 HIS A 217 PHE 0.015 0.001 PHE A 351 TYR 0.014 0.001 TYR A 264 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6283 (mm) REVERT: A 207 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5504 (tpt) REVERT: A 212 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6757 (mt-10) REVERT: A 328 GLU cc_start: 0.6200 (tp30) cc_final: 0.5507 (pt0) REVERT: A 386 PHE cc_start: 0.6801 (m-10) cc_final: 0.6085 (t80) REVERT: A 431 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7236 (tmtt) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.9906 time to fit residues: 69.1664 Evaluate side-chains 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3983 Z= 0.254 Angle : 0.545 9.616 5419 Z= 0.269 Chirality : 0.039 0.129 631 Planarity : 0.004 0.028 673 Dihedral : 6.915 66.672 566 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.81 % Allowed : 19.76 % 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: 1.94 (0.38), residues: 492 helix: 1.58 (0.27), residues: 369 sheet: -0.14 (1.77), residues: 10 loop : 0.70 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.002 PHE A 191 TYR 0.019 0.001 TYR A 264 ARG 0.001 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7677 (m-40) cc_final: 0.7288 (t0) REVERT: A 6 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6358 (mm) REVERT: A 207 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5465 (tpt) REVERT: A 212 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6829 (mt-10) REVERT: A 328 GLU cc_start: 0.6204 (tp30) cc_final: 0.5440 (tt0) REVERT: A 386 PHE cc_start: 0.6918 (m-10) cc_final: 0.6146 (t80) REVERT: A 431 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7227 (tmtm) REVERT: A 447 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7406 (mt-10) outliers start: 16 outliers final: 11 residues processed: 68 average time/residue: 0.8923 time to fit residues: 63.5052 Evaluate side-chains 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3983 Z= 0.147 Angle : 0.500 9.341 5419 Z= 0.244 Chirality : 0.036 0.125 631 Planarity : 0.003 0.027 673 Dihedral : 6.685 60.455 566 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.57 % Allowed : 20.24 % Favored : 76.19 % 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: 2.26 (0.39), residues: 492 helix: 1.77 (0.27), residues: 372 sheet: -0.09 (1.70), residues: 10 loop : 0.95 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.014 0.001 TYR A 264 ARG 0.003 0.000 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5536 (tpt) REVERT: A 212 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6685 (mt-10) REVERT: A 328 GLU cc_start: 0.6286 (tp30) cc_final: 0.5452 (pt0) REVERT: A 386 PHE cc_start: 0.6792 (m-10) cc_final: 0.6082 (t80) REVERT: A 431 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7215 (tmtt) REVERT: A 447 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7369 (mt-10) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.9985 time to fit residues: 68.6261 Evaluate side-chains 68 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.0000 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134190 restraints weight = 4317.360| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.02 r_work: 0.3368 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3983 Z= 0.134 Angle : 0.496 9.157 5419 Z= 0.240 Chirality : 0.036 0.125 631 Planarity : 0.003 0.026 673 Dihedral : 6.569 58.905 566 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.86 % Allowed : 20.95 % Favored : 76.19 % 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: 2.11 (0.39), residues: 492 helix: 1.70 (0.27), residues: 383 sheet: -0.22 (1.60), residues: 10 loop : 0.66 (0.68), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 213 HIS 0.001 0.000 HIS A 217 PHE 0.014 0.001 PHE A 351 TYR 0.014 0.001 TYR A 264 ARG 0.001 0.000 ARG A 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.35 seconds wall clock time: 30 minutes 21.46 seconds (1821.46 seconds total)