Starting phenix.real_space_refine on Fri May 9 15:22:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsw_36628/05_2025/8jsw_36628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsw_36628/05_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_36628/05_2025/8jsw_36628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsw_36628/05_2025/8jsw_36628.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsw_36628/05_2025/8jsw_36628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsw_36628/05_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-5687/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: 2.58, 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: 0.73 Conformation dependent library (CDL) restraints added in 357.2 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: 0.25 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: 0.87 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.810 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:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- 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= 0.544 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 Details of bonding type rmsd hydrogen bonds : bond 0.14787 ( 243) hydrogen bonds : angle 6.52591 ( 720) covalent geometry : bond 0.00868 ( 2928) covalent geometry : angle 0.91326 ( 3988) *********************** 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 : 0.295 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.9870 time to fit residues: 47.9640 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 : 0.301 ------------------------------------------------------------------------------- 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 = 42)----------------| | 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: 0.3137 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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= 0.163 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 Details of bonding type rmsd hydrogen bonds : bond 0.05561 ( 243) hydrogen bonds : angle 4.62137 ( 720) covalent geometry : bond 0.00359 ( 2928) covalent geometry : angle 0.68188 ( 3988) *********************** 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 : 0.303 Fit side-chains REVERT: A 196 SER cc_start: 0.8511 (t) cc_final: 0.8022 (m) REVERT: A 379 LYS cc_start: 0.7018 (tppp) cc_final: 0.6452 (mtmm) outliers start: 9 outliers final: 1 residues processed: 50 average time/residue: 1.0173 time to fit residues: 52.6017 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121787 restraints weight = 2996.719| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.25 r_work: 0.3118 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1154 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= 0.169 Angle : 0.682 9.112 3988 Z= 0.331 Chirality : 0.043 0.149 479 Planarity : 0.006 0.046 489 Dihedral : 4.170 17.293 405 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 19.00 % 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: 0.89 (0.43), residues: 380 helix: 1.13 (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 0.003 0.002 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.013 0.002 TYR A 422 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.05567 ( 243) hydrogen bonds : angle 4.48393 ( 720) covalent geometry : bond 0.00390 ( 2928) covalent geometry : angle 0.68157 ( 3988) *********************** 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 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.306 Fit side-chains REVERT: A 317 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 379 LYS cc_start: 0.6853 (tppp) cc_final: 0.6346 (mtmm) REVERT: A 435 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7149 (mt) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 1.1190 time to fit residues: 53.1531 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.0970 chunk 18 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.2732 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.148390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126288 restraints weight = 3038.996| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.32 r_work: 0.3178 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2928 Z= 0.129 Angle : 0.602 8.986 3988 Z= 0.290 Chirality : 0.040 0.147 479 Planarity : 0.006 0.045 489 Dihedral : 3.982 15.620 405 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.67 % Allowed : 21.33 % 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: 1.59 (0.44), residues: 380 helix: 1.60 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.74 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.007 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 243) hydrogen bonds : angle 4.22172 ( 720) covalent geometry : bond 0.00250 ( 2928) covalent geometry : angle 0.60169 ( 3988) *********************** 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 53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.327 Fit side-chains REVERT: A 306 MET cc_start: 0.8424 (ttp) cc_final: 0.8092 (ttt) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 1.0129 time to fit residues: 50.2841 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 0.0170 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.146708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124432 restraints weight = 2984.772| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.31 r_work: 0.3253 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2928 Z= 0.140 Angle : 0.642 9.189 3988 Z= 0.306 Chirality : 0.041 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 3.946 15.855 405 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.00 % Allowed : 20.00 % 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: 1.60 (0.45), residues: 380 helix: 1.62 (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 0.016 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 243) hydrogen bonds : angle 4.19120 ( 720) covalent geometry : bond 0.00301 ( 2928) covalent geometry : angle 0.64213 ( 3988) *********************** 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 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.302 Fit side-chains REVERT: A 317 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 12 outliers final: 5 residues processed: 46 average time/residue: 1.0223 time to fit residues: 48.5890 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 : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 0 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.139946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117004 restraints weight = 3054.052| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.32 r_work: 0.3058 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 2928 Z= 0.232 Angle : 0.770 9.495 3988 Z= 0.372 Chirality : 0.047 0.162 479 Planarity : 0.007 0.046 489 Dihedral : 4.288 18.430 405 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.62 (0.44), residues: 380 helix: 0.98 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -3.15 (0.78), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.005 0.002 HIS A 414 PHE 0.020 0.002 PHE A 429 TYR 0.020 0.002 TYR A 422 ARG 0.004 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.06675 ( 243) hydrogen bonds : angle 4.58388 ( 720) covalent geometry : bond 0.00584 ( 2928) covalent geometry : angle 0.77026 ( 3988) *********************** 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 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.278 Fit side-chains REVERT: A 351 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7278 (mp) REVERT: A 379 LYS cc_start: 0.6930 (tppp) cc_final: 0.6327 (mtmm) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 1.0207 time to fit residues: 54.7411 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.3926 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.144027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121511 restraints weight = 3125.107| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.33 r_work: 0.3140 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2928 Z= 0.138 Angle : 0.632 9.211 3988 Z= 0.302 Chirality : 0.040 0.149 479 Planarity : 0.006 0.045 489 Dihedral : 4.040 17.358 405 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.33 % Allowed : 21.67 % 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: 1.33 (0.45), residues: 380 helix: 1.48 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.21 (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 0.009 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 243) hydrogen bonds : angle 4.24568 ( 720) covalent geometry : bond 0.00284 ( 2928) covalent geometry : angle 0.63200 ( 3988) *********************** 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 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.299 Fit side-chains REVERT: A 267 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 379 LYS cc_start: 0.6636 (tppp) cc_final: 0.6027 (mtmm) REVERT: A 411 ASP cc_start: 0.8393 (m-30) cc_final: 0.8145 (m-30) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 1.1386 time to fit residues: 53.9446 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 23 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.144427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122093 restraints weight = 3039.662| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.31 r_work: 0.3295 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1666 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= 0.135 Angle : 0.623 9.251 3988 Z= 0.297 Chirality : 0.040 0.139 479 Planarity : 0.006 0.045 489 Dihedral : 3.878 16.038 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 23.00 % 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: 1.67 (0.45), residues: 380 helix: 1.68 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.02 (0.82), 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 0.014 0.001 PHE A 348 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 243) hydrogen bonds : angle 4.13443 ( 720) covalent geometry : bond 0.00284 ( 2928) covalent geometry : angle 0.62331 ( 3988) *********************** 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 to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.303 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 1.1122 time to fit residues: 50.4476 Evaluate side-chains 43 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 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 9 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.0030 chunk 0 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.146612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124436 restraints weight = 3051.598| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.32 r_work: 0.3225 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2928 Z= 0.137 Angle : 0.641 9.229 3988 Z= 0.306 Chirality : 0.040 0.142 479 Planarity : 0.006 0.044 489 Dihedral : 3.884 16.151 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.33 % Allowed : 23.00 % 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: 1.67 (0.45), residues: 380 helix: 1.69 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.96 (0.81), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 243) hydrogen bonds : angle 4.13415 ( 720) covalent geometry : bond 0.00294 ( 2928) covalent geometry : angle 0.64081 ( 3988) *********************** 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 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.300 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 43 average time/residue: 1.1703 time to fit residues: 51.8690 Evaluate side-chains 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 410 VAL 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: 0.7980 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.146626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124780 restraints weight = 3043.653| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.28 r_work: 0.3136 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1668 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= 0.152 Angle : 0.664 9.304 3988 Z= 0.317 Chirality : 0.041 0.139 479 Planarity : 0.006 0.045 489 Dihedral : 3.941 16.671 405 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.67 % Allowed : 22.67 % 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: 1.52 (0.45), residues: 380 helix: 1.57 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.89 (0.83), 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 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 243) hydrogen bonds : angle 4.21962 ( 720) covalent geometry : bond 0.00347 ( 2928) covalent geometry : angle 0.66427 ( 3988) ********************** 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: 5 poor density : 40 time to evaluate : 0.308 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 1.0913 time to fit residues: 48.4373 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 410 VAL Chi-restraints excluded: chain A residue 431 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122821 restraints weight = 3026.943| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.26 r_work: 0.3256 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1695 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= 0.150 Angle : 0.661 9.334 3988 Z= 0.315 Chirality : 0.041 0.145 479 Planarity : 0.006 0.045 489 Dihedral : 3.958 16.553 405 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 : 2.00 % Allowed : 22.67 % 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: 1.54 (0.45), residues: 380 helix: 1.58 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.83 (0.83), 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 0.015 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 243) hydrogen bonds : angle 4.23118 ( 720) covalent geometry : bond 0.00339 ( 2928) covalent geometry : angle 0.66122 ( 3988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2305.14 seconds wall clock time: 40 minutes 23.25 seconds (2423.25 seconds total)