Starting phenix.real_space_refine on Wed Mar 5 17:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrm_61760/03_2025/9jrm_61760_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrm_61760/03_2025/9jrm_61760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrm_61760/03_2025/9jrm_61760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrm_61760/03_2025/9jrm_61760.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrm_61760/03_2025/9jrm_61760_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrm_61760/03_2025/9jrm_61760_neut.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.081 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 12 5.16 5 C 2088 2.51 5 N 517 2.21 5 O 515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3134 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3090 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'GJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 0.92 Number of scatterers: 3134 At special positions: 0 Unit cell: (68, 67, 75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 2 15.00 O 515 8.00 N 517 7.00 C 2088 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: 0.97 Conformation dependent library (CDL) restraints added in 393.1 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 58 removed outlier: 4.084A pdb=" N GLN A 58 " --> pdb=" O PRO A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 68 through 91 removed outlier: 4.050A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.975A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.500A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.527A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.717A pdb=" N ILE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.874A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 264 through 293 removed outlier: 3.511A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 removed outlier: 3.905A pdb=" N ALA A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 391 removed outlier: 3.909A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 395 through 418 removed outlier: 3.605A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.556A pdb=" N GLY A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 702 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: 1.10 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.41: 1364 1.41 - 1.59: 1841 1.59 - 1.77: 4 1.77 - 1.95: 16 1.95 - 2.13: 2 Bond restraints: 3227 Sorted by residual: bond pdb=" O9 GJF A 701 " pdb=" P2 GJF A 701 " ideal model delta sigma weight residual 1.602 1.733 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C3 GJF A 701 " pdb=" N8 GJF A 701 " ideal model delta sigma weight residual 1.342 1.448 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 GJF A 701 " pdb=" C8 GJF A 701 " ideal model delta sigma weight residual 1.534 1.432 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C14 GJF A 701 " pdb=" N7 GJF A 701 " ideal model delta sigma weight residual 1.336 1.438 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C5 GJF A 701 " pdb=" C8 GJF A 701 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 3222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 4357 4.00 - 8.00: 33 8.00 - 12.00: 12 12.00 - 15.99: 4 15.99 - 19.99: 1 Bond angle restraints: 4407 Sorted by residual: angle pdb=" O3 GJF A 701 " pdb=" P1 GJF A 701 " pdb=" S1 GJF A 701 " ideal model delta sigma weight residual 97.13 117.12 -19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" O5 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sigma weight residual 116.54 101.01 15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O6 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sigma weight residual 98.38 111.04 -12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C6 GJF A 701 " pdb=" O1 GJF A 701 " pdb=" C7 GJF A 701 " ideal model delta sigma weight residual 110.83 98.67 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O5 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" O6 GJF A 701 " ideal model delta sigma weight residual 117.11 104.97 12.14 3.00e+00 1.11e-01 1.64e+01 ... (remaining 4402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 1643 20.96 - 41.91: 198 41.91 - 62.87: 29 62.87 - 83.83: 2 83.83 - 104.78: 7 Dihedral angle restraints: 1879 sinusoidal: 749 harmonic: 1130 Sorted by residual: dihedral pdb=" C9 GJF A 701 " pdb=" O6 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sinusoidal sigma weight residual -116.32 -11.54 -104.78 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG A 151 " pdb=" CD ARG A 151 " pdb=" NE ARG A 151 " pdb=" CZ ARG A 151 " ideal model delta sinusoidal sigma weight residual -90.00 -134.32 44.32 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 1876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 502 0.110 - 0.219: 10 0.219 - 0.329: 1 0.329 - 0.438: 2 0.438 - 0.548: 1 Chirality restraints: 516 Sorted by residual: chirality pdb=" P2 GJF A 701 " pdb=" O5 GJF A 701 " pdb=" O6 GJF A 701 " pdb=" O9 GJF A 701 " both_signs ideal model delta sigma weight residual True 2.71 3.26 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C16 GJF A 701 " pdb=" C15 GJF A 701 " pdb=" C17 GJF A 701 " pdb=" O8 GJF A 701 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C17 GJF A 701 " pdb=" C16 GJF A 701 " pdb=" C18 GJF A 701 " pdb=" O9 GJF A 701 " both_signs ideal model delta sigma weight residual False 2.60 2.25 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 513 not shown) Planarity restraints: 518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 82 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 84 " -0.008 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE A 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 84 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 84 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 84 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 84 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GJF A 701 " -0.012 2.00e-02 2.50e+03 6.80e-03 1.27e+00 pdb=" C11 GJF A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C12 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C13 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C14 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GJF A 701 " 0.012 2.00e-02 2.50e+03 pdb=" N3 GJF A 701 " -0.014 2.00e-02 2.50e+03 pdb=" N4 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" N5 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" N6 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GJF A 701 " 0.000 2.00e-02 2.50e+03 ... (remaining 515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 609 2.76 - 3.30: 3135 3.30 - 3.83: 5568 3.83 - 4.37: 6145 4.37 - 4.90: 10688 Nonbonded interactions: 26145 Sorted by model distance: nonbonded pdb=" O GLN A 172 " pdb=" OG1 THR A 176 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.236 3.040 nonbonded pdb=" O HIS A 358 " pdb=" OG SER A 361 " model vdw 2.332 3.040 nonbonded pdb=" NE2 GLN A 150 " pdb=" O VAL A 327 " model vdw 2.358 3.120 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.363 3.040 ... (remaining 26140 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: 1.900 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.630 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.007 0.131 3227 Z= 0.427 Angle : 1.013 19.992 4407 Z= 0.424 Chirality : 0.056 0.548 516 Planarity : 0.004 0.043 518 Dihedral : 17.940 104.782 1153 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 27.58 % Favored : 72.42 % 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: 0.97 (0.44), residues: 378 helix: 1.15 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -1.61 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 HIS 0.001 0.001 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.304 Fit side-chains REVERT: A 66 ASN cc_start: 0.8113 (m110) cc_final: 0.7905 (m110) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1167 time to fit residues: 5.4928 Evaluate side-chains 34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 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 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.188984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153922 restraints weight = 3541.313| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.83 r_work: 0.3620 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.201 Angle : 0.563 7.437 4407 Z= 0.275 Chirality : 0.039 0.155 516 Planarity : 0.004 0.044 518 Dihedral : 9.754 79.146 490 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.12 % Allowed : 26.97 % Favored : 70.91 % 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: 1.30 (0.43), residues: 378 helix: 1.36 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.354 Fit side-chains REVERT: A 65 THR cc_start: 0.8967 (p) cc_final: 0.8743 (p) REVERT: A 66 ASN cc_start: 0.7967 (m110) cc_final: 0.7697 (m110) REVERT: A 76 TYR cc_start: 0.8577 (t80) cc_final: 0.8236 (t80) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.1052 time to fit residues: 5.9873 Evaluate side-chains 39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150194 restraints weight = 3563.766| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.85 r_work: 0.3600 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3227 Z= 0.270 Angle : 0.568 7.498 4407 Z= 0.285 Chirality : 0.040 0.117 516 Planarity : 0.004 0.047 518 Dihedral : 8.889 76.121 490 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.55 % Allowed : 26.36 % Favored : 69.09 % 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: 1.21 (0.43), residues: 378 helix: 1.31 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.53 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.022 0.001 PHE A 84 TYR 0.013 0.002 TYR A 35 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.782 Fit side-chains REVERT: A 40 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: A 130 MET cc_start: 0.7697 (mmm) cc_final: 0.7467 (mtm) outliers start: 15 outliers final: 9 residues processed: 46 average time/residue: 0.0975 time to fit residues: 6.2513 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.0470 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154722 restraints weight = 3598.669| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.81 r_work: 0.3627 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.197 Angle : 0.536 7.538 4407 Z= 0.267 Chirality : 0.038 0.113 516 Planarity : 0.004 0.044 518 Dihedral : 8.259 74.134 490 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.55 % Allowed : 27.58 % Favored : 67.88 % 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: 1.51 (0.43), residues: 378 helix: 1.52 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.46 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.019 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.352 Fit side-chains REVERT: A 40 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: A 76 TYR cc_start: 0.8624 (t80) cc_final: 0.8233 (t80) REVERT: A 89 TYR cc_start: 0.7766 (t80) cc_final: 0.7490 (t80) outliers start: 15 outliers final: 11 residues processed: 48 average time/residue: 0.1663 time to fit residues: 10.7032 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.0010 chunk 19 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.188422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153288 restraints weight = 3533.433| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.83 r_work: 0.3633 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3227 Z= 0.193 Angle : 0.530 7.604 4407 Z= 0.264 Chirality : 0.038 0.113 516 Planarity : 0.004 0.044 518 Dihedral : 7.978 72.170 490 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.06 % Allowed : 26.36 % Favored : 67.58 % 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: 1.57 (0.44), residues: 378 helix: 1.58 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.64 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.019 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.309 Fit side-chains REVERT: A 40 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: A 76 TYR cc_start: 0.8574 (t80) cc_final: 0.8200 (t80) outliers start: 20 outliers final: 16 residues processed: 50 average time/residue: 0.0912 time to fit residues: 6.3453 Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.188461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153240 restraints weight = 3626.245| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.83 r_work: 0.3633 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3227 Z= 0.196 Angle : 0.539 7.655 4407 Z= 0.267 Chirality : 0.038 0.113 516 Planarity : 0.004 0.044 518 Dihedral : 7.840 70.614 490 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.55 % Allowed : 27.27 % Favored : 68.18 % 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: 1.69 (0.44), residues: 378 helix: 1.65 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.019 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.339 Fit side-chains REVERT: A 40 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: A 76 TYR cc_start: 0.8528 (t80) cc_final: 0.8222 (t80) outliers start: 15 outliers final: 13 residues processed: 46 average time/residue: 0.1020 time to fit residues: 6.4986 Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.187631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152597 restraints weight = 3534.141| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.81 r_work: 0.3624 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3227 Z= 0.214 Angle : 0.555 7.743 4407 Z= 0.273 Chirality : 0.039 0.128 516 Planarity : 0.004 0.045 518 Dihedral : 7.795 70.035 490 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.45 % Allowed : 26.97 % Favored : 67.58 % 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: 1.68 (0.44), residues: 378 helix: 1.64 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.302 Fit side-chains REVERT: A 40 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 76 TYR cc_start: 0.8549 (t80) cc_final: 0.8182 (t80) outliers start: 18 outliers final: 15 residues processed: 49 average time/residue: 0.0987 time to fit residues: 6.7255 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.189779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154226 restraints weight = 3594.097| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.87 r_work: 0.3640 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3227 Z= 0.175 Angle : 0.539 7.830 4407 Z= 0.263 Chirality : 0.038 0.154 516 Planarity : 0.004 0.043 518 Dihedral : 7.610 69.398 490 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.15 % Allowed : 27.27 % Favored : 67.58 % 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: 1.89 (0.44), residues: 378 helix: 1.80 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.42 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.018 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.314 Fit side-chains REVERT: A 40 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7090 (mp10) outliers start: 17 outliers final: 13 residues processed: 45 average time/residue: 0.0935 time to fit residues: 5.8884 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.186344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151442 restraints weight = 3581.863| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.81 r_work: 0.3614 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3227 Z= 0.243 Angle : 0.576 8.204 4407 Z= 0.282 Chirality : 0.040 0.179 516 Planarity : 0.004 0.045 518 Dihedral : 7.724 68.994 490 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.45 % Allowed : 26.97 % Favored : 67.58 % 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: 1.70 (0.43), residues: 378 helix: 1.67 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.46 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.022 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.342 Fit side-chains REVERT: A 40 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: A 76 TYR cc_start: 0.8514 (t80) cc_final: 0.8232 (t80) REVERT: A 89 TYR cc_start: 0.7723 (t80) cc_final: 0.7131 (t80) outliers start: 18 outliers final: 15 residues processed: 50 average time/residue: 0.0978 time to fit residues: 6.8144 Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.188333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153037 restraints weight = 3549.038| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.85 r_work: 0.3628 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3227 Z= 0.193 Angle : 0.559 8.594 4407 Z= 0.272 Chirality : 0.039 0.165 516 Planarity : 0.004 0.043 518 Dihedral : 7.629 68.752 490 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.55 % Allowed : 27.58 % Favored : 67.88 % 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: 1.88 (0.44), residues: 378 helix: 1.81 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -1.46 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 289 PHE 0.019 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.437 Fit side-chains REVERT: A 40 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 76 TYR cc_start: 0.8484 (t80) cc_final: 0.8200 (t80) REVERT: A 89 TYR cc_start: 0.7698 (t80) cc_final: 0.7081 (t80) outliers start: 15 outliers final: 14 residues processed: 48 average time/residue: 0.1029 time to fit residues: 6.8677 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.187313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152409 restraints weight = 3580.734| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.81 r_work: 0.3629 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.212 Angle : 0.568 8.426 4407 Z= 0.276 Chirality : 0.039 0.161 516 Planarity : 0.004 0.044 518 Dihedral : 7.614 68.449 490 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.45 % Allowed : 27.27 % Favored : 67.27 % 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: 1.83 (0.43), residues: 378 helix: 1.78 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -1.54 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.94 seconds wall clock time: 29 minutes 54.56 seconds (1794.56 seconds total)