Starting phenix.real_space_refine on Mon Feb 10 22:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7x_39831/02_2025/8z7x_39831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7x_39831/02_2025/8z7x_39831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7x_39831/02_2025/8z7x_39831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7x_39831/02_2025/8z7x_39831.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7x_39831/02_2025/8z7x_39831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7x_39831/02_2025/8z7x_39831.cif" } resolution = 3.36 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= 0.073 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 14 5.16 5 C 1992 2.51 5 N 442 2.21 5 O 507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2937 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 34 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: 2.82, per 1000 atoms: 0.95 Number of scatterers: 2955 At special positions: 0 Unit cell: (76.424, 58.716, 67.104, 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 14 16.00 O 507 8.00 N 442 7.00 C 1992 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: 0.81 Conformation dependent library (CDL) restraints added in 367.5 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 712 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 56 through 74 removed outlier: 3.842A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 78 through 100 removed outlier: 4.194A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.620A pdb=" N GLU A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.423A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 277 through 297 removed outlier: 3.560A pdb=" N ASN A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.605A pdb=" N ALA A 307 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 removed outlier: 3.502A pdb=" N VAL A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.979A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 398 removed outlier: 3.651A pdb=" N VAL A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.663A pdb=" N PHE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 Processing helix chain 'A' and resid 438 through 458 218 hydrogen bonds defined for protein. 651 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: 0.83 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 838 1.34 - 1.46: 578 1.46 - 1.57: 1601 1.57 - 1.69: 2 1.69 - 1.81: 23 Bond restraints: 3042 Sorted by residual: bond pdb=" C5 VIB A 501 " pdb=" S1 VIB A 501 " ideal model delta sigma weight residual 1.721 1.589 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C4A VIB A 501 " pdb=" N4A VIB A 501 " ideal model delta sigma weight residual 1.347 1.449 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C4 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.385 1.474 -0.089 2.00e-02 2.50e+03 2.00e+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 1.59e+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 8.35e+00 ... (remaining 3037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 3987 1.64 - 3.27: 131 3.27 - 4.91: 34 4.91 - 6.54: 9 6.54 - 8.18: 6 Bond angle restraints: 4167 Sorted by residual: angle pdb=" C TRP A 303 " pdb=" N ASP A 304 " pdb=" CA ASP A 304 " ideal model delta sigma weight residual 122.38 116.40 5.98 1.81e+00 3.05e-01 1.09e+01 angle pdb=" CD1 LEU A 302 " pdb=" CG LEU A 302 " pdb=" CD2 LEU A 302 " ideal model delta sigma weight residual 110.80 104.00 6.80 2.20e+00 2.07e-01 9.54e+00 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 109.81 116.40 -6.59 2.21e+00 2.05e-01 8.90e+00 angle pdb=" N VAL A 131 " pdb=" CA VAL A 131 " pdb=" C VAL A 131 " ideal model delta sigma weight residual 107.18 112.00 -4.82 1.73e+00 3.34e-01 7.76e+00 angle pdb=" C VAL A 423 " pdb=" N ILE A 424 " pdb=" CA ILE A 424 " ideal model delta sigma weight residual 121.65 117.57 4.08 1.48e+00 4.57e-01 7.58e+00 ... (remaining 4162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1555 17.12 - 34.24: 119 34.24 - 51.36: 34 51.36 - 68.49: 1 68.49 - 85.61: 4 Dihedral angle restraints: 1713 sinusoidal: 599 harmonic: 1114 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PRO A 193 " pdb=" C PRO A 193 " pdb=" N LYS A 194 " pdb=" CA LYS A 194 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -163.94 -16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 288 0.035 - 0.070: 124 0.070 - 0.105: 54 0.105 - 0.139: 15 0.139 - 0.174: 7 Chirality restraints: 488 Sorted by residual: chirality pdb=" CB ILE A 420 " pdb=" CA ILE A 420 " pdb=" CG1 ILE A 420 " pdb=" CG2 ILE A 420 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 485 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 56 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 57 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ILE A 51 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 51 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 52 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.009 2.00e-02 2.50e+03 9.41e-03 2.21e+00 pdb=" CG TRP A 281 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.001 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 249 2.74 - 3.28: 3184 3.28 - 3.82: 5170 3.82 - 4.36: 5733 4.36 - 4.90: 9879 Nonbonded interactions: 24215 Sorted by model distance: nonbonded pdb=" ND2 ASN A 53 " pdb=" OD1 ASN A 432 " model vdw 2.198 3.120 nonbonded pdb=" OE1 GLN A 300 " pdb=" ND2 ASN A 316 " model vdw 2.289 3.120 nonbonded pdb=" OE1 GLN A 438 " pdb=" OH TYR A 442 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.324 3.040 nonbonded pdb=" O PRO A 33 " pdb=" NE2 GLN A 300 " model vdw 2.364 3.120 ... (remaining 24210 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: 1.270 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: 0.020 Set scattering table: 0.030 Process input model: 12.640 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.006 0.132 3042 Z= 0.380 Angle : 0.795 8.177 4167 Z= 0.400 Chirality : 0.049 0.174 488 Planarity : 0.005 0.048 502 Dihedral : 13.906 85.607 1001 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.41), residues: 372 helix: 0.33 (0.29), residues: 283 sheet: None (None), residues: 0 loop : -2.57 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.001 0.000 HIS A 200 PHE 0.021 0.002 PHE A 189 TYR 0.019 0.002 TYR A 63 ARG 0.001 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.326 Fit side-chains REVERT: A 28 MET cc_start: 0.7780 (ttp) cc_final: 0.6942 (tmm) REVERT: A 96 LEU cc_start: 0.8532 (mt) cc_final: 0.8302 (mt) REVERT: A 437 ILE cc_start: 0.7332 (mp) cc_final: 0.7089 (tt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1152 time to fit residues: 6.8896 Evaluate side-chains 39 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.0060 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4352 r_free = 0.4352 target = 0.204602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179476 restraints weight = 2987.919| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.91 r_work: 0.4042 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3042 Z= 0.201 Angle : 0.589 5.700 4167 Z= 0.303 Chirality : 0.041 0.138 488 Planarity : 0.004 0.041 502 Dihedral : 6.151 82.774 411 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.98 % Allowed : 8.79 % Favored : 90.23 % 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: 0.17 (0.43), residues: 372 helix: 0.88 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -2.58 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 281 HIS 0.002 0.001 HIS A 135 PHE 0.016 0.001 PHE A 407 TYR 0.012 0.001 TYR A 14 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.303 Fit side-chains REVERT: A 38 TYR cc_start: 0.8694 (t80) cc_final: 0.8347 (t80) REVERT: A 96 LEU cc_start: 0.8655 (mt) cc_final: 0.8408 (mt) REVERT: A 137 GLN cc_start: 0.6595 (tt0) cc_final: 0.5733 (pm20) REVERT: A 403 TYR cc_start: 0.6647 (t80) cc_final: 0.6156 (t80) REVERT: A 424 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6658 (mp) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.1016 time to fit residues: 6.8001 Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4328 r_free = 0.4328 target = 0.201751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.176086 restraints weight = 2980.995| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.93 r_work: 0.4006 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3042 Z= 0.215 Angle : 0.576 5.604 4167 Z= 0.298 Chirality : 0.041 0.137 488 Planarity : 0.004 0.039 502 Dihedral : 6.070 83.188 411 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.30 % Allowed : 12.05 % Favored : 86.64 % 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: 0.41 (0.43), residues: 372 helix: 1.07 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.71 (0.61), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 90 TYR 0.009 0.001 TYR A 403 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.281 Fit side-chains REVERT: A 28 MET cc_start: 0.8013 (ttp) cc_final: 0.7282 (tmm) REVERT: A 96 LEU cc_start: 0.8725 (mt) cc_final: 0.8442 (mt) REVERT: A 137 GLN cc_start: 0.6639 (tt0) cc_final: 0.5726 (pm20) REVERT: A 403 TYR cc_start: 0.6667 (t80) cc_final: 0.6142 (t80) REVERT: A 424 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6577 (mp) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.1246 time to fit residues: 7.9348 Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.201499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176054 restraints weight = 3073.415| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.96 r_work: 0.3990 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3042 Z= 0.199 Angle : 0.574 5.529 4167 Z= 0.298 Chirality : 0.041 0.132 488 Planarity : 0.004 0.038 502 Dihedral : 6.040 84.321 411 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.95 % Allowed : 14.66 % Favored : 83.39 % 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: 0.56 (0.43), residues: 372 helix: 1.17 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.62 (0.61), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.001 PHE A 90 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.311 Fit side-chains REVERT: A 28 MET cc_start: 0.7925 (ttp) cc_final: 0.7187 (tmm) REVERT: A 96 LEU cc_start: 0.8737 (mt) cc_final: 0.8464 (mt) REVERT: A 137 GLN cc_start: 0.6612 (tt0) cc_final: 0.5693 (pm20) REVERT: A 403 TYR cc_start: 0.6671 (t80) cc_final: 0.6084 (t80) REVERT: A 424 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 429 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7877 (mtm-85) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1263 time to fit residues: 7.7758 Evaluate side-chains 44 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4291 r_free = 0.4291 target = 0.197857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.171424 restraints weight = 3081.270| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.94 r_work: 0.3939 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3042 Z= 0.267 Angle : 0.633 9.515 4167 Z= 0.322 Chirality : 0.042 0.141 488 Planarity : 0.004 0.038 502 Dihedral : 6.019 80.717 411 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.61 % Allowed : 14.33 % Favored : 83.06 % 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: 0.49 (0.43), residues: 372 helix: 1.10 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.59 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.010 0.001 TYR A 280 ARG 0.002 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.300 Fit side-chains REVERT: A 28 MET cc_start: 0.7944 (ttp) cc_final: 0.7384 (tmm) REVERT: A 96 LEU cc_start: 0.8735 (mt) cc_final: 0.8441 (mt) REVERT: A 403 TYR cc_start: 0.6802 (t80) cc_final: 0.6179 (t80) REVERT: A 424 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6594 (mp) REVERT: A 429 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7913 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 0.1281 time to fit residues: 8.2484 Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4289 r_free = 0.4289 target = 0.197793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171437 restraints weight = 3134.178| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.95 r_work: 0.3886 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3042 Z= 0.266 Angle : 0.627 8.212 4167 Z= 0.322 Chirality : 0.042 0.139 488 Planarity : 0.004 0.038 502 Dihedral : 6.002 79.966 411 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.95 % Allowed : 15.64 % Favored : 82.41 % 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: 0.45 (0.43), residues: 372 helix: 1.07 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.61 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 439 TYR 0.012 0.001 TYR A 280 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.300 Fit side-chains REVERT: A 28 MET cc_start: 0.7939 (ttp) cc_final: 0.7311 (tmm) REVERT: A 96 LEU cc_start: 0.8713 (mt) cc_final: 0.8431 (mt) REVERT: A 403 TYR cc_start: 0.6798 (t80) cc_final: 0.6276 (t80) REVERT: A 424 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6578 (mp) REVERT: A 429 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7916 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.1453 time to fit residues: 8.3635 Evaluate side-chains 46 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4271 r_free = 0.4271 target = 0.195998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.169868 restraints weight = 3055.559| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.91 r_work: 0.3929 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3042 Z= 0.280 Angle : 0.633 7.306 4167 Z= 0.326 Chirality : 0.042 0.141 488 Planarity : 0.004 0.038 502 Dihedral : 5.995 78.333 411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.28 % Allowed : 15.96 % Favored : 81.76 % 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: 0.40 (0.43), residues: 372 helix: 1.05 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.68 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.015 0.002 PHE A 439 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.299 Fit side-chains REVERT: A 28 MET cc_start: 0.7896 (ttp) cc_final: 0.7302 (tmm) REVERT: A 96 LEU cc_start: 0.8721 (mt) cc_final: 0.8439 (mt) REVERT: A 403 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6474 (t80) REVERT: A 424 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6576 (mp) REVERT: A 429 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7901 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1257 time to fit residues: 7.6987 Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 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 = 0.4320 r_free = 0.4320 target = 0.201131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.174948 restraints weight = 3064.219| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.95 r_work: 0.3992 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3042 Z= 0.195 Angle : 0.587 6.988 4167 Z= 0.304 Chirality : 0.040 0.127 488 Planarity : 0.004 0.037 502 Dihedral : 5.957 80.915 411 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.63 % Allowed : 16.61 % Favored : 81.76 % 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: 0.70 (0.43), residues: 372 helix: 1.27 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.62 (0.59), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.008 0.001 TYR A 280 ARG 0.001 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.314 Fit side-chains REVERT: A 28 MET cc_start: 0.7737 (ttp) cc_final: 0.7041 (tmm) REVERT: A 96 LEU cc_start: 0.8676 (mt) cc_final: 0.8420 (mt) REVERT: A 137 GLN cc_start: 0.6694 (tt0) cc_final: 0.5832 (pm20) REVERT: A 403 TYR cc_start: 0.6806 (t80) cc_final: 0.6298 (t80) REVERT: A 424 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6557 (mp) REVERT: A 429 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7993 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1260 time to fit residues: 8.2236 Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4300 r_free = 0.4300 target = 0.198491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172571 restraints weight = 3078.417| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.93 r_work: 0.3929 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3042 Z= 0.248 Angle : 0.616 6.675 4167 Z= 0.319 Chirality : 0.041 0.143 488 Planarity : 0.004 0.037 502 Dihedral : 5.947 79.793 411 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.63 % Allowed : 17.59 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.43), residues: 372 helix: 1.20 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.58 (0.60), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.014 0.001 PHE A 439 TYR 0.019 0.001 TYR A 305 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.308 Fit side-chains REVERT: A 28 MET cc_start: 0.7840 (ttp) cc_final: 0.7292 (tmm) REVERT: A 96 LEU cc_start: 0.8700 (mt) cc_final: 0.8431 (mt) REVERT: A 424 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6582 (mp) REVERT: A 429 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7940 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1296 time to fit residues: 7.8103 Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4254 r_free = 0.4254 target = 0.194104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168204 restraints weight = 3073.054| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.94 r_work: 0.3916 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3042 Z= 0.280 Angle : 0.648 6.596 4167 Z= 0.338 Chirality : 0.042 0.147 488 Planarity : 0.004 0.037 502 Dihedral : 5.963 77.606 411 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.63 % Allowed : 17.92 % Favored : 80.46 % 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: 0.48 (0.43), residues: 372 helix: 1.08 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -2.47 (0.61), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.014 0.002 PHE A 439 TYR 0.019 0.001 TYR A 305 ARG 0.001 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.297 Fit side-chains REVERT: A 28 MET cc_start: 0.7875 (ttp) cc_final: 0.7249 (tmm) REVERT: A 96 LEU cc_start: 0.8673 (mt) cc_final: 0.8400 (mt) REVERT: A 424 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6609 (mp) REVERT: A 429 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7938 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.1317 time to fit residues: 7.6889 Evaluate side-chains 45 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 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 = 0.4293 r_free = 0.4293 target = 0.197986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.172203 restraints weight = 3044.662| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.92 r_work: 0.3903 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3042 Z= 0.245 Angle : 0.623 6.517 4167 Z= 0.325 Chirality : 0.042 0.140 488 Planarity : 0.004 0.037 502 Dihedral : 5.928 77.917 411 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.28 % Allowed : 17.92 % Favored : 79.80 % 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: 0.53 (0.43), residues: 372 helix: 1.10 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.43 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.014 0.001 PHE A 439 TYR 0.018 0.001 TYR A 305 ARG 0.001 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.62 seconds wall clock time: 34 minutes 0.27 seconds (2040.27 seconds total)