Starting phenix.real_space_refine on Wed Mar 5 16:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7z_39833/03_2025/8z7z_39833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7z_39833/03_2025/8z7z_39833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7z_39833/03_2025/8z7z_39833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7z_39833/03_2025/8z7z_39833.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7z_39833/03_2025/8z7z_39833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7z_39833/03_2025/8z7z_39833.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.059 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 12 5.16 5 C 1886 2.51 5 N 436 2.21 5 O 500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 2834 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2816 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 1.00 Number of scatterers: 2834 At special positions: 0 Unit cell: (78.288, 68.036, 66.172, 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 12 16.00 O 500 8.00 N 436 7.00 C 1886 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: 0.84 Conformation dependent library (CDL) restraints added in 375.4 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 95 removed outlier: 5.443A pdb=" N TYR A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.783A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 3.666A pdb=" N ASP A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.855A pdb=" N LEU A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 137 through 145 removed outlier: 4.016A pdb=" N ILE A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.664A pdb=" N VAL A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.628A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 297' Processing helix chain 'A' and resid 298 through 324 removed outlier: 4.177A pdb=" N ASN A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.104A pdb=" N VAL A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.963A pdb=" N TRP A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N MET A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 443 removed outlier: 3.715A pdb=" N THR A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 483 removed outlier: 3.592A pdb=" N PHE A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 711 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: 0.78 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 849 1.34 - 1.46: 583 1.46 - 1.57: 1452 1.57 - 1.69: 2 1.69 - 1.81: 16 Bond restraints: 2902 Sorted by residual: bond pdb=" C5 VIB A 501 " pdb=" S1 VIB A 501 " ideal model delta sigma weight residual 1.721 1.591 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C4A VIB A 501 " pdb=" N4A VIB A 501 " ideal model delta sigma weight residual 1.347 1.453 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C4 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.385 1.476 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C2 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.315 1.395 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C4 VIB A 501 " pdb=" C5 VIB A 501 " ideal model delta sigma weight residual 1.358 1.416 -0.058 2.00e-02 2.50e+03 8.54e+00 ... (remaining 2897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3852 1.63 - 3.26: 108 3.26 - 4.88: 21 4.88 - 6.51: 11 6.51 - 8.14: 1 Bond angle restraints: 3993 Sorted by residual: angle pdb=" C CYS A 297 " pdb=" N TRP A 298 " pdb=" CA TRP A 298 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C2 VIB A 501 " pdb=" S1 VIB A 501 " pdb=" C5 VIB A 501 " ideal model delta sigma weight residual 91.25 99.39 -8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" C ASN A 71 " pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta sigma weight residual 121.54 116.45 5.09 1.91e+00 2.74e-01 7.10e+00 angle pdb=" C LEU A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 120.09 123.37 -3.28 1.25e+00 6.40e-01 6.89e+00 angle pdb=" CA TYR A 390 " pdb=" CB TYR A 390 " pdb=" CG TYR A 390 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.66e+00 ... (remaining 3988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 1502 16.67 - 33.33: 112 33.33 - 50.00: 19 50.00 - 66.66: 4 66.66 - 83.33: 4 Dihedral angle restraints: 1641 sinusoidal: 498 harmonic: 1143 Sorted by residual: dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N TYR A 97 " pdb=" CA TYR A 97 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU A 72 " pdb=" CG GLU A 72 " pdb=" CD GLU A 72 " pdb=" OE1 GLU A 72 " ideal model delta sinusoidal sigma weight residual 0.00 -83.33 83.33 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CA LYS A 322 " pdb=" CB LYS A 322 " pdb=" CG LYS A 322 " pdb=" CD LYS A 322 " ideal model delta sinusoidal sigma weight residual -60.00 -110.45 50.45 3 1.50e+01 4.44e-03 8.90e+00 ... (remaining 1638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 342 0.039 - 0.079: 122 0.079 - 0.118: 25 0.118 - 0.158: 5 0.158 - 0.197: 3 Chirality restraints: 497 Sorted by residual: chirality pdb=" CG LEU A 82 " pdb=" CB LEU A 82 " pdb=" CD1 LEU A 82 " pdb=" CD2 LEU A 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CB ILE A 331 " pdb=" CA ILE A 331 " pdb=" CG1 ILE A 331 " pdb=" CG2 ILE A 331 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CB ILE A 386 " pdb=" CA ILE A 386 " pdb=" CG1 ILE A 386 " pdb=" CG2 ILE A 386 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 494 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 390 " -0.021 2.00e-02 2.50e+03 1.94e-02 7.52e+00 pdb=" CG TYR A 390 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 390 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 390 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 390 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 390 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 390 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 390 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 298 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C TRP A 298 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 298 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 299 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 50 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 51 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.029 5.00e-02 4.00e+02 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 88 2.72 - 3.26: 3143 3.26 - 3.81: 4976 3.81 - 4.35: 5756 4.35 - 4.90: 9634 Nonbonded interactions: 23597 Sorted by model distance: nonbonded pdb=" O LEU A 304 " pdb=" OH TYR A 462 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A 173 " pdb=" O GLY A 334 " model vdw 2.176 3.040 nonbonded pdb=" O VAL A 312 " pdb=" OG1 THR A 316 " model vdw 2.230 3.040 nonbonded pdb=" ND2 ASN A 71 " pdb=" O VAL A 443 " model vdw 2.307 3.120 nonbonded pdb=" OE2 GLU A 50 " pdb=" OH TYR A 131 " model vdw 2.311 3.040 ... (remaining 23592 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: 2.880 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.760 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 0.005 0.130 2902 Z= 0.347 Angle : 0.710 8.140 3993 Z= 0.364 Chirality : 0.044 0.197 497 Planarity : 0.005 0.053 484 Dihedral : 13.231 83.330 907 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.43), residues: 385 helix: 1.00 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -1.25 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 301 PHE 0.027 0.002 PHE A 396 TYR 0.048 0.002 TYR A 390 ARG 0.003 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.266 Fit side-chains REVERT: A 96 ARG cc_start: 0.4145 (mmt180) cc_final: 0.3932 (mmt180) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1125 time to fit residues: 13.1269 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 435 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.237443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.217910 restraints weight = 3611.969| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 1.95 r_work: 0.4468 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2902 Z= 0.207 Angle : 0.575 5.353 3993 Z= 0.309 Chirality : 0.039 0.114 497 Planarity : 0.005 0.049 484 Dihedral : 5.620 72.442 418 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 12.98 % Favored : 84.73 % 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: 1.09 (0.42), residues: 385 helix: 1.29 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.37 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 PHE 0.020 0.002 PHE A 89 TYR 0.050 0.002 TYR A 390 ARG 0.002 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.299 Fit side-chains REVERT: A 96 ARG cc_start: 0.3814 (mmt180) cc_final: 0.3522 (mmt180) REVERT: A 108 LEU cc_start: 0.7378 (mt) cc_final: 0.6898 (mt) REVERT: A 138 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5326 (mm-30) outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 0.1249 time to fit residues: 11.9524 Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4733 r_free = 0.4733 target = 0.235678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.216724 restraints weight = 3665.184| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 1.84 r_work: 0.4464 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2902 Z= 0.214 Angle : 0.569 5.163 3993 Z= 0.306 Chirality : 0.039 0.121 497 Planarity : 0.005 0.050 484 Dihedral : 5.445 68.492 418 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.82 % Allowed : 17.56 % Favored : 78.63 % 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: 1.32 (0.42), residues: 385 helix: 1.52 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -1.55 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 PHE 0.023 0.002 PHE A 89 TYR 0.048 0.002 TYR A 390 ARG 0.001 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.374 Fit side-chains REVERT: A 96 ARG cc_start: 0.4053 (mmt180) cc_final: 0.3704 (mmt180) REVERT: A 108 LEU cc_start: 0.7402 (mt) cc_final: 0.6908 (mt) REVERT: A 138 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5387 (mm-30) REVERT: A 392 SER cc_start: 0.7202 (p) cc_final: 0.6668 (t) outliers start: 10 outliers final: 4 residues processed: 86 average time/residue: 0.1377 time to fit residues: 14.5517 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.235877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.217334 restraints weight = 3655.550| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 1.79 r_work: 0.4476 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2902 Z= 0.204 Angle : 0.550 5.125 3993 Z= 0.297 Chirality : 0.039 0.110 497 Planarity : 0.005 0.050 484 Dihedral : 5.268 64.163 418 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.91 % Allowed : 19.47 % Favored : 78.63 % 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: 1.56 (0.43), residues: 385 helix: 1.63 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.34 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 PHE 0.024 0.002 PHE A 89 TYR 0.045 0.002 TYR A 390 ARG 0.001 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.282 Fit side-chains REVERT: A 96 ARG cc_start: 0.4065 (mmt180) cc_final: 0.3761 (mmt180) REVERT: A 108 LEU cc_start: 0.7359 (mt) cc_final: 0.6869 (mt) REVERT: A 138 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5442 (mm-30) outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 0.1267 time to fit residues: 12.8597 Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.234801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.215281 restraints weight = 3702.683| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 1.94 r_work: 0.4452 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2902 Z= 0.239 Angle : 0.596 7.390 3993 Z= 0.313 Chirality : 0.040 0.152 497 Planarity : 0.005 0.052 484 Dihedral : 5.306 62.455 418 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.05 % Allowed : 20.61 % Favored : 76.34 % 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 (0.42), residues: 385 helix: 1.53 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.46 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 PHE 0.021 0.002 PHE A 89 TYR 0.038 0.002 TYR A 390 ARG 0.001 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.275 Fit side-chains REVERT: A 96 ARG cc_start: 0.4084 (mmt180) cc_final: 0.3782 (mmt180) REVERT: A 138 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5492 (mm-30) REVERT: A 337 GLU cc_start: 0.6408 (mm-30) cc_final: 0.5996 (mm-30) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.1263 time to fit residues: 12.7667 Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.237807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.218392 restraints weight = 3772.384| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 1.97 r_work: 0.4476 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2902 Z= 0.198 Angle : 0.561 5.485 3993 Z= 0.299 Chirality : 0.039 0.155 497 Planarity : 0.005 0.053 484 Dihedral : 5.128 61.120 418 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.67 % Allowed : 23.66 % Favored : 73.66 % 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: 1.73 (0.43), residues: 385 helix: 1.71 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.11 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 PHE 0.022 0.002 PHE A 89 TYR 0.030 0.002 TYR A 390 ARG 0.000 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.305 Fit side-chains REVERT: A 96 ARG cc_start: 0.4083 (mmt180) cc_final: 0.3769 (mmt180) REVERT: A 108 LEU cc_start: 0.7371 (mt) cc_final: 0.6836 (mt) REVERT: A 138 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5642 (mt-10) REVERT: A 337 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5895 (mm-30) outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.1299 time to fit residues: 12.8068 Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.235195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.215428 restraints weight = 3768.196| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 1.97 r_work: 0.4452 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2902 Z= 0.226 Angle : 0.587 5.174 3993 Z= 0.313 Chirality : 0.040 0.163 497 Planarity : 0.005 0.055 484 Dihedral : 5.165 60.820 418 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.44 % Allowed : 23.28 % Favored : 73.28 % 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 (0.43), residues: 385 helix: 1.66 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.00 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 PHE 0.024 0.002 PHE A 89 TYR 0.036 0.002 TYR A 400 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.242 Fit side-chains REVERT: A 96 ARG cc_start: 0.4016 (mmt180) cc_final: 0.3771 (mmt180) REVERT: A 466 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7443 (tt) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.1069 time to fit residues: 10.1702 Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.236661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.217443 restraints weight = 3698.920| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 1.93 r_work: 0.4467 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2902 Z= 0.203 Angle : 0.569 5.152 3993 Z= 0.303 Chirality : 0.039 0.164 497 Planarity : 0.005 0.057 484 Dihedral : 5.100 60.471 418 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.05 % Allowed : 23.28 % Favored : 73.66 % 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: 1.71 (0.43), residues: 385 helix: 1.69 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.07 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 112 PHE 0.023 0.002 PHE A 89 TYR 0.028 0.002 TYR A 390 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.324 Fit side-chains REVERT: A 96 ARG cc_start: 0.4100 (mmt180) cc_final: 0.3846 (mmt180) REVERT: A 108 LEU cc_start: 0.7317 (mt) cc_final: 0.6819 (mt) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.1197 time to fit residues: 11.8760 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.238584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.218963 restraints weight = 3651.994| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 1.96 r_work: 0.4479 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2902 Z= 0.209 Angle : 0.580 7.768 3993 Z= 0.310 Chirality : 0.039 0.165 497 Planarity : 0.005 0.058 484 Dihedral : 5.208 60.177 418 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.29 % Allowed : 24.05 % Favored : 73.66 % 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: 1.66 (0.43), residues: 385 helix: 1.65 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.09 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 112 PHE 0.025 0.002 PHE A 89 TYR 0.025 0.002 TYR A 390 ARG 0.001 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.281 Fit side-chains REVERT: A 96 ARG cc_start: 0.4083 (mmt180) cc_final: 0.3825 (mmt180) REVERT: A 108 LEU cc_start: 0.7419 (mt) cc_final: 0.6867 (mt) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.1282 time to fit residues: 12.2008 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4748 r_free = 0.4748 target = 0.237522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.218071 restraints weight = 3716.700| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 1.97 r_work: 0.4474 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2902 Z= 0.206 Angle : 0.598 7.704 3993 Z= 0.318 Chirality : 0.039 0.173 497 Planarity : 0.005 0.059 484 Dihedral : 5.188 60.028 418 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.05 % Allowed : 24.05 % Favored : 72.90 % 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: 1.62 (0.42), residues: 385 helix: 1.64 (0.28), residues: 307 sheet: None (None), residues: 0 loop : -1.15 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 112 PHE 0.027 0.002 PHE A 89 TYR 0.025 0.002 TYR A 390 ARG 0.001 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.300 Fit side-chains REVERT: A 96 ARG cc_start: 0.3973 (mmt180) cc_final: 0.3699 (mmt180) REVERT: A 108 LEU cc_start: 0.7418 (mt) cc_final: 0.6956 (mt) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.1169 time to fit residues: 11.1093 Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.237061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.217638 restraints weight = 3651.832| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 1.94 r_work: 0.4473 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2902 Z= 0.205 Angle : 0.609 7.930 3993 Z= 0.320 Chirality : 0.039 0.173 497 Planarity : 0.005 0.059 484 Dihedral : 5.213 59.899 418 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 24.81 % Favored : 72.52 % 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: 1.63 (0.42), residues: 385 helix: 1.65 (0.28), residues: 307 sheet: None (None), residues: 0 loop : -1.15 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 112 PHE 0.027 0.002 PHE A 89 TYR 0.026 0.002 TYR A 390 ARG 0.001 0.000 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.44 seconds wall clock time: 29 minutes 6.99 seconds (1746.99 seconds total)