Starting phenix.real_space_refine on Mon Jan 13 19:00:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y66_38968/01_2025/8y66_38968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y66_38968/01_2025/8y66_38968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y66_38968/01_2025/8y66_38968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y66_38968/01_2025/8y66_38968.map" model { file = "/net/cci-nas-00/data/ceres_data/8y66_38968/01_2025/8y66_38968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y66_38968/01_2025/8y66_38968.cif" } resolution = 3.28 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= 0.008 sd= 0.100 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 15 5.16 5 C 2385 2.51 5 N 580 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3606 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3586 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.72 Number of scatterers: 3606 At special positions: 0 Unit cell: (83.3525, 63.8675, 70.3625, 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 15 16.00 O 626 8.00 N 580 7.00 C 2385 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: 0.89 Conformation dependent library (CDL) restraints added in 411.1 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 54 through 76 removed outlier: 4.222A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 102 through 136 removed outlier: 4.716A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.774A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.647A pdb=" N GLY A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 4.454A pdb=" N VAL A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.930A pdb=" N GLU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 331 through 346 removed outlier: 6.386A pdb=" N ASN A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 352 through 379 removed outlier: 4.010A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.942A pdb=" N LEU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 429 removed outlier: 3.570A pdb=" N LEU A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.668A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 476 removed outlier: 3.546A pdb=" N GLY A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 480 through 498 removed outlier: 4.527A pdb=" N PHE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.652A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 831 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: 1.01 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 548 1.31 - 1.44: 1011 1.44 - 1.56: 2116 1.56 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3697 Sorted by residual: bond pdb=" CAS AGI A 601 " pdb=" OAL AGI A 601 " ideal model delta sigma weight residual 1.350 1.494 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" CAJ AGI A 601 " pdb=" CAQ AGI A 601 " ideal model delta sigma weight residual 1.354 1.485 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" CAO AGI A 601 " pdb=" OAD AGI A 601 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CAQ AGI A 601 " pdb=" OAL AGI A 601 " ideal model delta sigma weight residual 1.341 1.461 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CAM AGI A 601 " pdb=" OAB AGI A 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 3692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 4912 2.07 - 4.14: 94 4.14 - 6.21: 23 6.21 - 8.29: 7 8.29 - 10.36: 2 Bond angle restraints: 5038 Sorted by residual: angle pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " pdb=" CG PHE A 235 " ideal model delta sigma weight residual 113.80 121.43 -7.63 1.00e+00 1.00e+00 5.83e+01 angle pdb=" N PHE A 235 " pdb=" CA PHE A 235 " pdb=" C PHE A 235 " ideal model delta sigma weight residual 112.59 104.30 8.29 1.22e+00 6.72e-01 4.61e+01 angle pdb=" C LEU A 234 " pdb=" N PHE A 235 " pdb=" CA PHE A 235 " ideal model delta sigma weight residual 122.67 112.31 10.36 1.59e+00 3.96e-01 4.24e+01 angle pdb=" N LEU A 234 " pdb=" CA LEU A 234 " pdb=" C LEU A 234 " ideal model delta sigma weight residual 112.90 104.60 8.30 1.31e+00 5.83e-01 4.02e+01 angle pdb=" C PHE A 235 " pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " ideal model delta sigma weight residual 111.02 118.18 -7.16 1.61e+00 3.86e-01 1.98e+01 ... (remaining 5033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1924 17.77 - 35.54: 191 35.54 - 53.31: 26 53.31 - 71.07: 4 71.07 - 88.84: 3 Dihedral angle restraints: 2148 sinusoidal: 818 harmonic: 1330 Sorted by residual: dihedral pdb=" CA ASP A 102 " pdb=" C ASP A 102 " pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta harmonic sigma weight residual -180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU A 292 " pdb=" CG GLU A 292 " pdb=" CD GLU A 292 " pdb=" OE1 GLU A 292 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 447 " pdb=" CD ARG A 447 " pdb=" NE ARG A 447 " pdb=" CZ ARG A 447 " ideal model delta sinusoidal sigma weight residual -90.00 -132.68 42.68 2 1.50e+01 4.44e-03 9.80e+00 ... (remaining 2145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 397 0.041 - 0.082: 153 0.082 - 0.123: 32 0.123 - 0.164: 9 0.164 - 0.206: 1 Chirality restraints: 592 Sorted by residual: chirality pdb=" CA PHE A 235 " pdb=" N PHE A 235 " pdb=" C PHE A 235 " pdb=" CB PHE A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 589 not shown) Planarity restraints: 623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " 0.026 2.00e-02 2.50e+03 5.48e-02 3.01e+01 pdb=" C TYR A 233 " -0.095 2.00e-02 2.50e+03 pdb=" O TYR A 233 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 234 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 469 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO A 470 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 235 " 0.023 2.00e-02 2.50e+03 1.83e-02 5.83e+00 pdb=" CG PHE A 235 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 235 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 235 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 235 " 0.006 2.00e-02 2.50e+03 ... (remaining 620 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 638 2.76 - 3.29: 3715 3.29 - 3.83: 6081 3.83 - 4.36: 6485 4.36 - 4.90: 11514 Nonbonded interactions: 28433 Sorted by model distance: nonbonded pdb=" OE1 GLU A 191 " pdb=" OG SER A 255 " model vdw 2.223 3.040 nonbonded pdb=" O VAL A 356 " pdb=" OG SER A 359 " model vdw 2.269 3.040 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.278 3.040 nonbonded pdb=" OE2 GLU A 501 " pdb=" NH1 ARG A 505 " model vdw 2.381 3.120 nonbonded pdb=" O GLU A 223 " pdb=" NZ LYS A 227 " model vdw 2.388 3.120 ... (remaining 28428 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: 0.540 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 0.144 3697 Z= 0.377 Angle : 0.765 10.358 5038 Z= 0.436 Chirality : 0.045 0.206 592 Planarity : 0.006 0.075 623 Dihedral : 14.110 88.841 1300 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % 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: 1.27 (0.41), residues: 465 helix: 1.14 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.19 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.002 0.001 HIS A 139 PHE 0.042 0.002 PHE A 235 TYR 0.011 0.001 TYR A 327 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.359 Fit side-chains REVERT: A 102 ASP cc_start: 0.6624 (p0) cc_final: 0.6207 (p0) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1009 time to fit residues: 10.2193 Evaluate side-chains 63 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.225912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.187868 restraints weight = 4383.628| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.12 r_work: 0.4112 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3697 Z= 0.204 Angle : 0.586 5.745 5038 Z= 0.304 Chirality : 0.043 0.139 592 Planarity : 0.005 0.050 623 Dihedral : 4.265 13.879 507 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.34 % Allowed : 9.90 % Favored : 87.76 % 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: 1.26 (0.41), residues: 465 helix: 1.16 (0.28), residues: 384 sheet: None (None), residues: 0 loop : -0.39 (0.77), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.002 PHE A 164 TYR 0.008 0.001 TYR A 327 ARG 0.001 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.405 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1109 time to fit residues: 10.8700 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 489 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.224839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.187287 restraints weight = 4364.420| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.02 r_work: 0.4109 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3697 Z= 0.194 Angle : 0.584 10.267 5038 Z= 0.295 Chirality : 0.043 0.167 592 Planarity : 0.004 0.039 623 Dihedral : 4.143 12.436 507 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.65 % Allowed : 12.24 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.41), residues: 465 helix: 1.29 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.33 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.021 0.002 PHE A 514 TYR 0.011 0.001 TYR A 188 ARG 0.006 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.417 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1038 time to fit residues: 10.4405 Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.226019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187696 restraints weight = 4392.056| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 3.13 r_work: 0.4104 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3697 Z= 0.189 Angle : 0.573 6.674 5038 Z= 0.290 Chirality : 0.043 0.147 592 Planarity : 0.004 0.037 623 Dihedral : 4.048 12.295 507 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.39 % Allowed : 14.32 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.41), residues: 465 helix: 1.38 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.35 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.016 0.002 PHE A 208 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.376 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.0995 time to fit residues: 9.3583 Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.187365 restraints weight = 4497.020| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.14 r_work: 0.4108 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3697 Z= 0.175 Angle : 0.542 5.358 5038 Z= 0.279 Chirality : 0.043 0.146 592 Planarity : 0.004 0.036 623 Dihedral : 3.977 12.491 507 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.65 % Allowed : 15.10 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.41), residues: 465 helix: 1.50 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.29 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.016 0.001 PHE A 208 TYR 0.012 0.001 TYR A 188 ARG 0.002 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.370 Fit side-chains REVERT: A 126 LEU cc_start: 0.8710 (mm) cc_final: 0.8395 (mp) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.1070 time to fit residues: 10.3045 Evaluate side-chains 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.226192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.188324 restraints weight = 4494.551| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.14 r_work: 0.4154 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3697 Z= 0.166 Angle : 0.534 5.319 5038 Z= 0.275 Chirality : 0.042 0.146 592 Planarity : 0.004 0.035 623 Dihedral : 3.915 12.028 507 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.69 % Allowed : 15.36 % Favored : 79.95 % 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: 1.84 (0.41), residues: 465 helix: 1.57 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.19 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.026 0.001 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.002 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.389 Fit side-chains REVERT: A 126 LEU cc_start: 0.8672 (mm) cc_final: 0.8335 (mp) outliers start: 18 outliers final: 11 residues processed: 74 average time/residue: 0.0971 time to fit residues: 9.8876 Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.225522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.187914 restraints weight = 4421.730| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 3.10 r_work: 0.4155 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.172 Angle : 0.551 5.434 5038 Z= 0.283 Chirality : 0.043 0.175 592 Planarity : 0.004 0.035 623 Dihedral : 3.898 11.840 507 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.69 % Allowed : 15.62 % Favored : 79.69 % 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 (0.41), residues: 465 helix: 1.61 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.17 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.001 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.407 Fit side-chains REVERT: A 102 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5719 (p0) REVERT: A 126 LEU cc_start: 0.8646 (mm) cc_final: 0.8312 (mp) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.0940 time to fit residues: 9.4228 Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 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 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.223438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.185490 restraints weight = 4464.273| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.13 r_work: 0.4129 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3697 Z= 0.203 Angle : 0.574 5.579 5038 Z= 0.293 Chirality : 0.043 0.148 592 Planarity : 0.004 0.036 623 Dihedral : 3.973 11.619 507 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.43 % Allowed : 16.67 % Favored : 78.91 % 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: 1.75 (0.41), residues: 465 helix: 1.52 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.26 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.002 PHE A 164 TYR 0.011 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.383 Fit side-chains REVERT: A 102 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5799 (p0) REVERT: A 126 LEU cc_start: 0.8683 (mm) cc_final: 0.8343 (mp) outliers start: 17 outliers final: 14 residues processed: 70 average time/residue: 0.1011 time to fit residues: 9.8323 Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.224143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186476 restraints weight = 4379.939| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.09 r_work: 0.4134 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3697 Z= 0.187 Angle : 0.579 6.692 5038 Z= 0.293 Chirality : 0.043 0.155 592 Planarity : 0.004 0.036 623 Dihedral : 3.972 11.649 507 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.69 % Allowed : 16.15 % Favored : 79.17 % 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 (0.41), residues: 465 helix: 1.60 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.26 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.026 0.001 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.517 Fit side-chains REVERT: A 102 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5721 (p0) REVERT: A 126 LEU cc_start: 0.8598 (mm) cc_final: 0.8248 (mp) outliers start: 18 outliers final: 15 residues processed: 72 average time/residue: 0.1034 time to fit residues: 10.3403 Evaluate side-chains 73 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.187967 restraints weight = 4417.743| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 3.09 r_work: 0.4152 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3697 Z= 0.170 Angle : 0.583 7.977 5038 Z= 0.295 Chirality : 0.043 0.169 592 Planarity : 0.004 0.036 623 Dihedral : 3.977 11.544 507 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.43 % Allowed : 16.15 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.41), residues: 465 helix: 1.63 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.26 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.001 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.398 Fit side-chains REVERT: A 102 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5736 (p0) REVERT: A 126 LEU cc_start: 0.8570 (mm) cc_final: 0.8238 (mp) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.1018 time to fit residues: 9.8174 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.222315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.185002 restraints weight = 4529.295| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.23 r_work: 0.4132 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.196 Angle : 0.601 8.275 5038 Z= 0.303 Chirality : 0.043 0.169 592 Planarity : 0.004 0.036 623 Dihedral : 3.987 11.883 507 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.91 % Allowed : 17.19 % Favored : 78.91 % 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: 1.82 (0.41), residues: 465 helix: 1.60 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.31 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.001 PHE A 164 TYR 0.017 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.85 seconds wall clock time: 34 minutes 31.72 seconds (2071.72 seconds total)