Starting phenix.real_space_refine on Thu Jul 18 18:30:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsw_36628/07_2024/8jsw_36628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsw_36628/07_2024/8jsw_36628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsw_36628/07_2024/8jsw_36628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsw_36628/07_2024/8jsw_36628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsw_36628/07_2024/8jsw_36628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsw_36628/07_2024/8jsw_36628.cif" } resolution = 2.84 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= -0.002 sd= 0.123 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 27 5.16 5 C 1906 2.51 5 N 443 2.21 5 O 483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2859 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2846 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.75, per 1000 atoms: 0.96 Number of scatterers: 2859 At special positions: 0 Unit cell: (57.8, 63.75, 71.4, 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 27 16.00 O 483 8.00 N 443 7.00 C 1906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.95 Conformation dependent library (CDL) restraints added in 933.6 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 3.608A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.508A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.988A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.661A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.857A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 3.511A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.681A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.687A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.604A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.855A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.653A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.542A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 1.15 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: 450 1.32 - 1.45: 734 1.45 - 1.57: 1696 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 2928 Sorted by residual: bond pdb=" CE2 SRO A 501 " pdb=" CZ2 SRO A 501 " ideal model delta sigma weight residual 1.393 1.576 -0.183 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CD2 SRO A 501 " pdb=" CE3 SRO A 501 " ideal model delta sigma weight residual 1.404 1.575 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" CZ2 SRO A 501 " pdb=" CH2 SRO A 501 " ideal model delta sigma weight residual 1.386 1.506 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CE3 SRO A 501 " pdb=" CZ3 SRO A 501 " ideal model delta sigma weight residual 1.385 1.505 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CZ3 SRO A 501 " pdb=" CH2 SRO A 501 " ideal model delta sigma weight residual 1.407 1.486 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 2923 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 116 106.69 - 113.52: 1593 113.52 - 120.35: 1186 120.35 - 127.18: 1064 127.18 - 134.02: 29 Bond angle restraints: 3988 Sorted by residual: angle pdb=" N PRO A 473 " pdb=" CA PRO A 473 " pdb=" C PRO A 473 " ideal model delta sigma weight residual 110.70 116.98 -6.28 1.22e+00 6.72e-01 2.65e+01 angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" N PRO A 45 " ideal model delta sigma weight residual 120.83 123.61 -2.78 6.10e-01 2.69e+00 2.08e+01 angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 120.83 123.41 -2.58 6.10e-01 2.69e+00 1.79e+01 angle pdb=" CA PRO A 473 " pdb=" C PRO A 473 " pdb=" N PRO A 474 " ideal model delta sigma weight residual 117.93 122.87 -4.94 1.20e+00 6.94e-01 1.70e+01 angle pdb=" CA ILE A 381 " pdb=" C ILE A 381 " pdb=" O ILE A 381 " ideal model delta sigma weight residual 121.05 116.88 4.17 1.04e+00 9.25e-01 1.61e+01 ... (remaining 3983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1532 17.78 - 35.56: 139 35.56 - 53.34: 33 53.34 - 71.12: 3 71.12 - 88.90: 2 Dihedral angle restraints: 1709 sinusoidal: 623 harmonic: 1086 Sorted by residual: dihedral pdb=" C ILE A 44 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual -122.00 -131.84 9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual 123.40 131.84 -8.44 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 317 0.043 - 0.086: 108 0.086 - 0.129: 40 0.129 - 0.173: 8 0.173 - 0.216: 6 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA PRO A 473 " pdb=" N PRO A 473 " pdb=" C PRO A 473 " pdb=" CB PRO A 473 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 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 2.22 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 443 " pdb=" N ILE A 443 " pdb=" C ILE A 443 " pdb=" CB ILE A 443 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 476 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 400 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C SER A 400 " -0.037 2.00e-02 2.50e+03 pdb=" O SER A 400 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 401 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 401 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C SER A 401 " -0.035 2.00e-02 2.50e+03 pdb=" O SER A 401 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 402 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 186 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C LEU A 186 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 186 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 187 " -0.011 2.00e-02 2.50e+03 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 688 2.80 - 3.33: 2847 3.33 - 3.85: 4502 3.85 - 4.38: 5222 4.38 - 4.90: 9244 Nonbonded interactions: 22503 Sorted by model distance: nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.277 2.440 nonbonded pdb=" O TRP A 318 " pdb=" OG1 THR A 322 " model vdw 2.296 2.440 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.430 2.440 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.437 2.520 nonbonded pdb=" O ILE A 367 " pdb=" OG SER A 371 " model vdw 2.469 2.440 ... (remaining 22498 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.030 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.009 0.183 2928 Z= 0.588 Angle : 0.913 6.722 3988 Z= 0.632 Chirality : 0.054 0.216 479 Planarity : 0.006 0.046 489 Dihedral : 14.545 88.899 1017 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.67 % Allowed : 21.67 % Favored : 77.67 % 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: -0.02 (0.42), residues: 380 helix: 0.54 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -2.82 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.002 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.228 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.8563 time to fit residues: 41.6536 Evaluate side-chains 45 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2928 Z= 0.252 Angle : 0.702 9.064 3988 Z= 0.341 Chirality : 0.043 0.151 479 Planarity : 0.006 0.047 489 Dihedral : 4.462 20.235 407 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.33 % Allowed : 20.33 % Favored : 76.33 % 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: 0.54 (0.42), residues: 380 helix: 0.89 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.57 (0.72), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.003 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.308 Fit side-chains REVERT: A 317 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8209 (mt) REVERT: A 379 LYS cc_start: 0.6940 (tppp) cc_final: 0.6740 (mtmm) outliers start: 10 outliers final: 1 residues processed: 50 average time/residue: 0.9910 time to fit residues: 51.1595 Evaluate side-chains 44 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2928 Z= 0.243 Angle : 0.672 9.275 3988 Z= 0.326 Chirality : 0.043 0.150 479 Planarity : 0.006 0.046 489 Dihedral : 4.160 17.817 405 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % 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: 0.81 (0.43), residues: 380 helix: 1.07 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.83 (0.77), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.003 0.002 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.306 Fit side-chains REVERT: A 317 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 435 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7482 (mt) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 1.0345 time to fit residues: 49.1460 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2928 Z= 0.232 Angle : 0.659 9.246 3988 Z= 0.319 Chirality : 0.042 0.148 479 Planarity : 0.006 0.045 489 Dihedral : 4.101 17.331 405 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.33 % Allowed : 20.00 % Favored : 75.67 % 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: 0.98 (0.44), residues: 380 helix: 1.20 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.98 (0.78), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.296 Fit side-chains REVERT: A 317 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8173 (mt) REVERT: A 435 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7531 (mt) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.9932 time to fit residues: 51.2655 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0050 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2928 Z= 0.182 Angle : 0.632 9.183 3988 Z= 0.303 Chirality : 0.040 0.146 479 Planarity : 0.006 0.045 489 Dihedral : 3.996 16.983 405 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.67 % Allowed : 20.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.44), residues: 380 helix: 1.44 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.92 (0.79), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.365 Fit side-chains REVERT: A 317 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 351 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 379 LYS cc_start: 0.6616 (tppp) cc_final: 0.6374 (mtmm) outliers start: 14 outliers final: 7 residues processed: 52 average time/residue: 0.9191 time to fit residues: 49.4191 Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2928 Z= 0.233 Angle : 0.663 9.256 3988 Z= 0.318 Chirality : 0.042 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 4.048 17.447 405 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.33 % Allowed : 20.67 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.44), residues: 380 helix: 1.35 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.11 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.017 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.298 Fit side-chains REVERT: A 351 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7654 (mp) REVERT: A 379 LYS cc_start: 0.6639 (tppp) cc_final: 0.6361 (mtmm) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.0572 time to fit residues: 51.2282 Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2928 Z= 0.206 Angle : 0.645 9.281 3988 Z= 0.309 Chirality : 0.041 0.145 479 Planarity : 0.006 0.045 489 Dihedral : 4.013 17.233 405 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.67 % Allowed : 21.67 % Favored : 74.67 % 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: 1.30 (0.44), residues: 380 helix: 1.44 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.11 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.264 Fit side-chains REVERT: A 351 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 379 LYS cc_start: 0.6602 (tppp) cc_final: 0.6379 (mtmm) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.9855 time to fit residues: 49.8349 Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0770 chunk 3 optimal weight: 7.9990 chunk 28 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2928 Z= 0.176 Angle : 0.624 9.264 3988 Z= 0.298 Chirality : 0.040 0.143 479 Planarity : 0.006 0.045 489 Dihedral : 3.935 16.845 405 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.33 % Allowed : 23.33 % Favored : 74.33 % 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: 1.53 (0.45), residues: 380 helix: 1.60 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.08 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.316 Fit side-chains REVERT: A 351 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7637 (mp) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 1.0466 time to fit residues: 47.5043 Evaluate side-chains 44 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8341 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2928 Z= 0.257 Angle : 0.706 9.395 3988 Z= 0.339 Chirality : 0.043 0.145 479 Planarity : 0.006 0.044 489 Dihedral : 4.080 17.368 405 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.00 % Allowed : 23.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.44), residues: 380 helix: 1.34 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.14 (0.80), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.004 0.002 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.289 Fit side-chains REVERT: A 351 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7656 (mp) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 1.0082 time to fit residues: 50.0009 Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2928 Z= 0.211 Angle : 0.677 9.325 3988 Z= 0.325 Chirality : 0.041 0.147 479 Planarity : 0.006 0.045 489 Dihedral : 4.035 17.304 405 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.33 % Allowed : 24.33 % Favored : 73.33 % 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: 1.34 (0.45), residues: 380 helix: 1.46 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.99 (0.80), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.003 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.316 Fit side-chains REVERT: A 351 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7646 (mp) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.0494 time to fit residues: 48.7297 Evaluate side-chains 46 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.144364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121989 restraints weight = 3060.443| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.32 r_work: 0.3294 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2928 Z= 0.203 Angle : 0.662 9.319 3988 Z= 0.318 Chirality : 0.041 0.142 479 Planarity : 0.006 0.045 489 Dihedral : 3.991 17.111 405 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.33 % Allowed : 24.33 % Favored : 73.33 % 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: 1.41 (0.45), residues: 380 helix: 1.50 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.95 (0.81), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.31 seconds wall clock time: 29 minutes 29.66 seconds (1769.66 seconds total)