Starting phenix.real_space_refine on Wed Mar 5 16:42:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsw_36628/03_2025/8jsw_36628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsw_36628/03_2025/8jsw_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/cci-nas-00/data/ceres_data/8jsw_36628/03_2025/8jsw_36628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsw_36628/03_2025/8jsw_36628.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsw_36628/03_2025/8jsw_36628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsw_36628/03_2025/8jsw_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. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 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: 2.56, per 1000 atoms: 0.90 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 336.6 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: 0.26 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: 0.73 Time building geometry restraints manager: 0.84 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: 0.00 - 1.34: 3562 1.34 - 2.69: 320 2.69 - 4.03: 78 4.03 - 5.38: 22 5.38 - 6.72: 6 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 3.040 nonbonded pdb=" O TRP A 318 " pdb=" OG1 THR A 322 " model vdw 2.296 3.040 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.430 3.040 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.437 3.120 nonbonded pdb=" O ILE A 367 " pdb=" OG SER A 371 " model vdw 2.469 3.040 ... (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: 1.450 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.660 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.302 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 1.0083 time to fit residues: 48.9545 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122698 restraints weight = 3017.115| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.31 r_work: 0.3136 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2928 Z= 0.223 Angle : 0.682 8.957 3988 Z= 0.333 Chirality : 0.042 0.153 479 Planarity : 0.006 0.047 489 Dihedral : 4.440 20.104 407 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.00 % Allowed : 19.67 % Favored : 77.33 % 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: 0.84 (0.43), residues: 380 helix: 1.07 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.38 (0.75), residues: 54 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 0.001 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.002 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 to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.275 Fit side-chains REVERT: A 196 SER cc_start: 0.8511 (t) cc_final: 0.8022 (m) REVERT: A 379 LYS cc_start: 0.7016 (tppp) cc_final: 0.6451 (mtmm) outliers start: 9 outliers final: 1 residues processed: 50 average time/residue: 1.0264 time to fit residues: 52.9752 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120950 restraints weight = 2996.879| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.25 r_work: 0.3113 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2928 Z= 0.254 Angle : 0.688 9.086 3988 Z= 0.334 Chirality : 0.043 0.148 479 Planarity : 0.006 0.046 489 Dihedral : 4.186 17.413 405 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.67 % Allowed : 18.67 % 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: 0.84 (0.43), residues: 380 helix: 1.09 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.84 (0.79), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.004 0.002 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.014 0.002 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 to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.299 Fit side-chains REVERT: A 317 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7934 (mt) REVERT: A 379 LYS cc_start: 0.6887 (tppp) cc_final: 0.6388 (mtmm) REVERT: A 435 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7149 (mt) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 1.1201 time to fit residues: 53.1187 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121988 restraints weight = 3039.677| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.27 r_work: 0.3118 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1282 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= 0.238 Angle : 0.664 9.224 3988 Z= 0.322 Chirality : 0.042 0.148 479 Planarity : 0.006 0.045 489 Dihedral : 4.141 17.080 405 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.67 % Allowed : 20.00 % 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: 1.01 (0.44), residues: 380 helix: 1.22 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.93 (0.78), residues: 50 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 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.274 Fit side-chains REVERT: A 317 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 435 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7216 (mt) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 1.0473 time to fit residues: 50.8346 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 15 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.146120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124534 restraints weight = 2985.437| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.24 r_work: 0.3243 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2928 Z= 0.186 Angle : 0.633 9.187 3988 Z= 0.305 Chirality : 0.040 0.146 479 Planarity : 0.006 0.045 489 Dihedral : 4.025 16.577 405 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.00 % Allowed : 19.67 % 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: 1.40 (0.44), residues: 380 helix: 1.48 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.94 (0.80), residues: 48 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 0.015 0.001 PHE A 238 TYR 0.010 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 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.280 Fit side-chains REVERT: A 317 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7962 (mt) REVERT: A 351 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7240 (mp) REVERT: A 379 LYS cc_start: 0.6686 (tppp) cc_final: 0.6088 (mtmm) outliers start: 12 outliers final: 5 residues processed: 50 average time/residue: 1.0084 time to fit residues: 52.0766 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122554 restraints weight = 3047.789| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.28 r_work: 0.3225 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2928 Z= 0.221 Angle : 0.659 9.245 3988 Z= 0.315 Chirality : 0.042 0.144 479 Planarity : 0.006 0.044 489 Dihedral : 4.047 16.984 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.09 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: 1.24 (0.44), residues: 380 helix: 1.40 (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 0.016 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 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 to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.306 Fit side-chains REVERT: A 317 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7954 (mt) REVERT: A 351 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7267 (mp) REVERT: A 379 LYS cc_start: 0.6691 (tppp) cc_final: 0.6110 (mtmm) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.0979 time to fit residues: 53.2355 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120241 restraints weight = 3127.149| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.33 r_work: 0.3216 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1534 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= 0.216 Angle : 0.649 9.257 3988 Z= 0.311 Chirality : 0.041 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 4.025 16.929 405 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.67 % Allowed : 21.00 % Favored : 75.33 % 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: 1.27 (0.45), residues: 380 helix: 1.42 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.09 (0.80), 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 0.015 0.001 PHE A 238 TYR 0.013 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 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.309 Fit side-chains REVERT: A 351 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7284 (mp) REVERT: A 379 LYS cc_start: 0.6724 (tppp) cc_final: 0.6149 (mtmm) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.9986 time to fit residues: 52.6680 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119906 restraints weight = 3036.124| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.31 r_work: 0.3118 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1576 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= 0.223 Angle : 0.658 9.317 3988 Z= 0.317 Chirality : 0.041 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 4.027 16.978 405 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.67 % Allowed : 22.00 % 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: 1.26 (0.44), residues: 380 helix: 1.41 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.12 (0.80), 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 0.014 0.001 TYR A 422 ARG 0.002 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 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.282 Fit side-chains REVERT: A 351 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7125 (mp) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 1.0098 time to fit residues: 52.1163 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 overall best weight: 0.4326 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121856 restraints weight = 3047.198| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.31 r_work: 0.3146 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2928 Z= 0.182 Angle : 0.649 9.259 3988 Z= 0.311 Chirality : 0.040 0.144 479 Planarity : 0.006 0.044 489 Dihedral : 3.957 16.644 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 22.67 % 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: 1.54 (0.45), residues: 380 helix: 1.61 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.05 (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 0.015 0.001 PHE A 238 TYR 0.010 0.001 TYR A 422 ARG 0.001 0.000 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 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.328 Fit side-chains REVERT: A 351 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7108 (mp) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 1.0571 time to fit residues: 48.0990 Evaluate side-chains 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.144063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122144 restraints weight = 3046.819| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.26 r_work: 0.3302 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1650 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= 0.224 Angle : 0.676 9.347 3988 Z= 0.324 Chirality : 0.041 0.141 479 Planarity : 0.006 0.044 489 Dihedral : 4.004 16.910 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.00 % Allowed : 23.00 % 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: 1.39 (0.44), residues: 380 helix: 1.49 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.00 (0.81), 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 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.316 Fit side-chains REVERT: A 351 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7443 (mp) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 1.0536 time to fit residues: 45.6965 Evaluate side-chains 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0020 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.146568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124958 restraints weight = 3020.151| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.25 r_work: 0.3341 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2928 Z= 0.176 Angle : 0.636 9.257 3988 Z= 0.303 Chirality : 0.040 0.144 479 Planarity : 0.006 0.044 489 Dihedral : 3.904 16.196 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.00 % Allowed : 23.00 % 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: 1.76 (0.45), residues: 380 helix: 1.73 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.77 (0.83), 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 348 TYR 0.009 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: 2282.76 seconds wall clock time: 39 minutes 43.78 seconds (2383.78 seconds total)