Starting phenix.real_space_refine on Mon Feb 10 21:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7z_39833/02_2025/8z7z_39833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7z_39833/02_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_39833/02_2025/8z7z_39833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7z_39833/02_2025/8z7z_39833.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7z_39833/02_2025/8z7z_39833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7z_39833/02_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-5592/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: 2.42, per 1000 atoms: 0.85 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: 0.77 Conformation dependent library (CDL) restraints added in 374.4 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: 0.22 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: 0.84 Time building geometry restraints manager: 0.90 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: 1.150 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.910 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- 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 : 0.302 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: 0.1165 time to fit residues: 13.5710 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 : 0.310 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.4741 r_free = 0.4741 target = 0.237157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.217570 restraints weight = 3612.293| |-----------------------------------------------------------------------------| r_work (start): 0.4582 rms_B_bonded: 1.96 r_work: 0.4467 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1897 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= 0.205 Angle : 0.576 5.222 3993 Z= 0.309 Chirality : 0.039 0.111 497 Planarity : 0.005 0.050 484 Dihedral : 5.601 71.786 418 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 13.36 % Favored : 84.35 % 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: 1.06 (0.42), residues: 385 helix: 1.26 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.36 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 PHE 0.022 0.002 PHE A 396 TYR 0.049 0.002 TYR A 390 ARG 0.001 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 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.235 Fit side-chains REVERT: A 96 ARG cc_start: 0.3847 (mmt180) cc_final: 0.3547 (mmt180) REVERT: A 108 LEU cc_start: 0.7417 (mt) cc_final: 0.6936 (mt) REVERT: A 138 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5331 (mm-30) outliers start: 6 outliers final: 2 residues processed: 81 average time/residue: 0.1323 time to fit residues: 13.1671 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 : 0.324 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.4729 r_free = 0.4729 target = 0.235442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.216508 restraints weight = 3665.610| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 1.84 r_work: 0.4467 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2244 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= 0.215 Angle : 0.566 5.155 3993 Z= 0.305 Chirality : 0.039 0.118 497 Planarity : 0.005 0.050 484 Dihedral : 5.446 68.548 418 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.44 % Allowed : 19.08 % Favored : 77.48 % 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 (0.42), residues: 385 helix: 1.52 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -1.56 (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 90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.291 Fit side-chains REVERT: A 96 ARG cc_start: 0.4066 (mmt180) cc_final: 0.3713 (mmt180) REVERT: A 108 LEU cc_start: 0.7403 (mt) cc_final: 0.6910 (mt) REVERT: A 138 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5387 (mm-30) REVERT: A 317 GLN cc_start: 0.7308 (mm-40) cc_final: 0.7108 (mt0) REVERT: A 392 SER cc_start: 0.7205 (p) cc_final: 0.6667 (t) outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 0.1306 time to fit residues: 13.4911 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.233217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.214367 restraints weight = 3651.538| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 1.80 r_work: 0.4448 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2902 Z= 0.228 Angle : 0.579 5.190 3993 Z= 0.311 Chirality : 0.040 0.152 497 Planarity : 0.005 0.051 484 Dihedral : 5.344 64.973 418 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.05 % Allowed : 20.23 % Favored : 76.72 % 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: 1.42 (0.43), residues: 385 helix: 1.53 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.37 (0.70), 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 0.047 0.002 TYR A 390 ARG 0.002 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 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.309 Fit side-chains REVERT: A 96 ARG cc_start: 0.4082 (mmt180) cc_final: 0.3768 (mmt180) REVERT: A 138 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5424 (mm-30) REVERT: A 435 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5529 (tt0) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.1241 time to fit residues: 12.2181 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4720 r_free = 0.4720 target = 0.233348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.214090 restraints weight = 3706.252| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 1.87 r_work: 0.4451 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2902 Z= 0.245 Angle : 0.603 6.828 3993 Z= 0.317 Chirality : 0.040 0.157 497 Planarity : 0.005 0.052 484 Dihedral : 5.332 62.978 418 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.20 % Allowed : 20.99 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.42), residues: 385 helix: 1.51 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.48 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 PHE 0.024 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: 11 poor density : 77 time to evaluate : 0.301 Fit side-chains REVERT: A 96 ARG cc_start: 0.4135 (mmt180) cc_final: 0.3825 (mmt180) REVERT: A 337 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6109 (mm-30) REVERT: A 435 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5436 (tt0) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.1268 time to fit residues: 12.6863 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL 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 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 435 GLN 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: 0.0470 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.4769 r_free = 0.4769 target = 0.239104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.220451 restraints weight = 3752.420| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 1.90 r_work: 0.4532 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2902 Z= 0.174 Angle : 0.548 5.173 3993 Z= 0.294 Chirality : 0.038 0.156 497 Planarity : 0.005 0.052 484 Dihedral : 5.134 62.130 418 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: 1.71 (0.43), residues: 385 helix: 1.72 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.17 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 112 PHE 0.025 0.002 PHE A 89 TYR 0.027 0.001 TYR A 390 ARG 0.000 0.000 ARG A 162 *********************** 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 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.290 Fit side-chains REVERT: A 96 ARG cc_start: 0.4100 (mmt180) cc_final: 0.3804 (mmt180) REVERT: A 108 LEU cc_start: 0.7302 (mt) cc_final: 0.6770 (mt) REVERT: A 138 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5607 (mt-10) REVERT: A 337 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5890 (mm-30) REVERT: A 435 GLN cc_start: 0.5606 (OUTLIER) cc_final: 0.5251 (tm-30) outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.1186 time to fit residues: 11.9404 Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 435 GLN 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: 0.7980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.0060 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.237012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.217438 restraints weight = 3768.162| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 1.97 r_work: 0.4468 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3418 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= 0.201 Angle : 0.579 6.915 3993 Z= 0.305 Chirality : 0.040 0.166 497 Planarity : 0.005 0.056 484 Dihedral : 5.125 62.255 418 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.05 % Allowed : 22.52 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.43), residues: 385 helix: 1.65 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -0.92 (0.79), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 PHE 0.021 0.002 PHE A 89 TYR 0.035 0.002 TYR A 400 ARG 0.001 0.000 ARG A 162 *********************** 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 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.304 Fit side-chains REVERT: A 96 ARG cc_start: 0.4094 (mmt180) cc_final: 0.3834 (mmt180) REVERT: A 108 LEU cc_start: 0.7329 (mt) cc_final: 0.6739 (mt) REVERT: A 435 GLN cc_start: 0.5806 (OUTLIER) cc_final: 0.5496 (tm-30) outliers start: 8 outliers final: 3 residues processed: 75 average time/residue: 0.1217 time to fit residues: 11.4258 Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 435 GLN 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: 0.9980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4722 r_free = 0.4722 target = 0.233680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.214377 restraints weight = 3728.274| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 1.94 r_work: 0.4437 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2902 Z= 0.249 Angle : 0.601 5.145 3993 Z= 0.319 Chirality : 0.041 0.178 497 Planarity : 0.005 0.057 484 Dihedral : 5.179 61.979 418 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: 1.56 (0.43), residues: 385 helix: 1.60 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.17 (0.76), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 112 PHE 0.022 0.002 PHE A 89 TYR 0.029 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 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.300 Fit side-chains REVERT: A 96 ARG cc_start: 0.4162 (mmt180) cc_final: 0.3852 (mmt180) REVERT: A 435 GLN cc_start: 0.5921 (OUTLIER) cc_final: 0.5552 (tt0) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.1333 time to fit residues: 12.0589 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 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 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 = 0.4740 r_free = 0.4740 target = 0.236675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.217687 restraints weight = 3648.808| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 1.90 r_work: 0.4473 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3636 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= 0.211 Angle : 0.584 7.783 3993 Z= 0.309 Chirality : 0.040 0.159 497 Planarity : 0.005 0.058 484 Dihedral : 5.141 61.565 418 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 24.43 % 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: 1.55 (0.43), residues: 385 helix: 1.58 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.18 (0.76), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 298 PHE 0.021 0.002 PHE A 89 TYR 0.026 0.002 TYR A 390 ARG 0.002 0.000 ARG A 397 *********************** 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 : 0.287 Fit side-chains REVERT: A 96 ARG cc_start: 0.4136 (mmt180) cc_final: 0.3827 (mmt180) REVERT: A 435 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5349 (tt0) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.1216 time to fit residues: 11.6287 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 435 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4688 r_free = 0.4688 target = 0.230578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.211360 restraints weight = 3736.820| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.90 r_work: 0.4417 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2902 Z= 0.293 Angle : 0.666 7.193 3993 Z= 0.347 Chirality : 0.043 0.173 497 Planarity : 0.005 0.058 484 Dihedral : 5.288 61.236 418 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 23.28 % Favored : 74.05 % 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: 1.23 (0.43), residues: 385 helix: 1.38 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.33 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 298 PHE 0.025 0.003 PHE A 89 TYR 0.029 0.002 TYR A 390 ARG 0.004 0.001 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: 7 poor density : 75 time to evaluate : 0.283 Fit side-chains REVERT: A 96 ARG cc_start: 0.4126 (mmt180) cc_final: 0.3803 (mmt180) REVERT: A 435 GLN cc_start: 0.5902 (OUTLIER) cc_final: 0.5497 (tt0) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.1314 time to fit residues: 12.3580 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4725 r_free = 0.4725 target = 0.234587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.215529 restraints weight = 3681.935| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 1.91 r_work: 0.4455 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3825 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= 0.226 Angle : 0.628 7.003 3993 Z= 0.330 Chirality : 0.041 0.164 497 Planarity : 0.005 0.062 484 Dihedral : 5.248 60.099 418 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.91 % Allowed : 24.05 % Favored : 74.05 % 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: 1.43 (0.43), residues: 385 helix: 1.54 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.27 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 298 PHE 0.025 0.002 PHE A 89 TYR 0.026 0.002 TYR A 390 ARG 0.003 0.000 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.27 seconds wall clock time: 29 minutes 10.30 seconds (1750.30 seconds total)