Starting phenix.real_space_refine on Wed Mar 5 22:06:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqq_60388/03_2025/8zqq_60388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqq_60388/03_2025/8zqq_60388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqq_60388/03_2025/8zqq_60388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqq_60388/03_2025/8zqq_60388.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqq_60388/03_2025/8zqq_60388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqq_60388/03_2025/8zqq_60388.cif" } resolution = 2.5 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= 0.101 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2559 2.51 5 N 575 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3836 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3788 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 469} Chain breaks: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' CL': 1, ' NA': 1, 'CHT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.53, per 1000 atoms: 0.92 Number of scatterers: 3836 At special positions: 0 Unit cell: (87.55, 67.15, 87.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 1 11.00 O 680 8.00 N 575 7.00 C 2559 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 459.6 milliseconds 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 77.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.806A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 71 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.715A pdb=" N SER A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 158 removed outlier: 4.026A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.586A pdb=" N GLY A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.524A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.544A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.876A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 removed outlier: 4.044A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 6.178A pdb=" N ASN A 301 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 363 removed outlier: 4.023A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 410 through 427 removed outlier: 4.404A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.938A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 503 removed outlier: 3.635A pdb=" N LEU A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 270 hydrogen bonds defined for protein. 795 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: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1109 1.34 - 1.46: 822 1.46 - 1.58: 1975 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3941 Sorted by residual: bond pdb=" CA LYS A 104 " pdb=" C LYS A 104 " ideal model delta sigma weight residual 1.524 1.561 -0.038 1.26e-02 6.30e+03 8.86e+00 bond pdb=" C LYS A 104 " pdb=" N PRO A 105 " ideal model delta sigma weight residual 1.335 1.367 -0.033 1.19e-02 7.06e+03 7.64e+00 bond pdb=" C PRO A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.335 1.367 -0.033 1.19e-02 7.06e+03 7.58e+00 bond pdb=" C GLU A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.25e-02 6.40e+03 5.78e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.58e+00 ... (remaining 3936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 5269 1.85 - 3.70: 87 3.70 - 5.56: 20 5.56 - 7.41: 3 7.41 - 9.26: 5 Bond angle restraints: 5384 Sorted by residual: angle pdb=" N THR A 506 " pdb=" CA THR A 506 " pdb=" C THR A 506 " ideal model delta sigma weight residual 108.67 100.65 8.02 1.67e+00 3.59e-01 2.31e+01 angle pdb=" N LEU A 507 " pdb=" CA LEU A 507 " pdb=" C LEU A 507 " ideal model delta sigma weight residual 109.58 117.00 -7.42 1.75e+00 3.27e-01 1.80e+01 angle pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta sigma weight residual 119.56 115.72 3.84 1.01e+00 9.80e-01 1.44e+01 angle pdb=" CA THR A 506 " pdb=" C THR A 506 " pdb=" N LEU A 507 " ideal model delta sigma weight residual 119.98 116.81 3.17 8.50e-01 1.38e+00 1.39e+01 angle pdb=" C PRO A 508 " pdb=" N PRO A 509 " pdb=" CA PRO A 509 " ideal model delta sigma weight residual 119.56 116.54 3.02 1.02e+00 9.61e-01 8.78e+00 ... (remaining 5379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 2103 21.90 - 43.80: 132 43.80 - 65.70: 23 65.70 - 87.60: 11 87.60 - 109.50: 4 Dihedral angle restraints: 2273 sinusoidal: 858 harmonic: 1415 Sorted by residual: dihedral pdb=" CA THR A 312 " pdb=" C THR A 312 " pdb=" N THR A 313 " pdb=" CA THR A 313 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.21 109.50 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" CA TRP A 228 " pdb=" C TRP A 228 " pdb=" N LEU A 229 " pdb=" CA LEU A 229 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 2270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 525 0.056 - 0.111: 99 0.111 - 0.166: 8 0.166 - 0.222: 1 0.222 - 0.277: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LEU A 507 " pdb=" N LEU A 507 " pdb=" C LEU A 507 " pdb=" CB LEU A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA PRO A 509 " pdb=" N PRO A 509 " pdb=" C PRO A 509 " pdb=" CB PRO A 509 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 631 not shown) Planarity restraints: 649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 309 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.71e+00 pdb=" N PRO A 310 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 508 " 0.007 2.00e-02 2.50e+03 1.29e-02 1.68e+00 pdb=" C PRO A 508 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO A 508 " 0.008 2.00e-02 2.50e+03 pdb=" N PRO A 509 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 359 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C PHE A 359 " -0.022 2.00e-02 2.50e+03 pdb=" O PHE A 359 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA A 360 " 0.007 2.00e-02 2.50e+03 ... (remaining 646 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 409 2.75 - 3.29: 3687 3.29 - 3.82: 6399 3.82 - 4.36: 7322 4.36 - 4.90: 12990 Nonbonded interactions: 30807 Sorted by model distance: nonbonded pdb=" O VAL A 63 " pdb="NA NA A 602 " model vdw 2.211 2.470 nonbonded pdb=" OG SER A 346 " pdb="NA NA A 602 " model vdw 2.257 2.470 nonbonded pdb=" OE2 GLU A 138 " pdb=" OG SER A 354 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP A 242 " pdb=" OG1 THR A 481 " model vdw 2.314 3.040 nonbonded pdb=" O ALA A 60 " pdb="NA NA A 602 " model vdw 2.323 2.470 ... (remaining 30802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.770 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.003 0.038 3941 Z= 0.209 Angle : 0.652 9.262 5384 Z= 0.341 Chirality : 0.042 0.277 634 Planarity : 0.004 0.033 648 Dihedral : 16.305 109.502 1377 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.25 % Allowed : 11.81 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.76 (0.39), residues: 486 helix: 1.89 (0.28), residues: 358 sheet: -2.57 (1.51), residues: 10 loop : -0.69 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.002 0.001 HIS A 221 PHE 0.008 0.001 PHE A 488 TYR 0.012 0.001 TYR A 496 ARG 0.000 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.407 Fit side-chains REVERT: A 263 SER cc_start: 0.7881 (m) cc_final: 0.7486 (p) REVERT: A 451 GLU cc_start: 0.8464 (tp30) cc_final: 0.8197 (tp30) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 1.1505 time to fit residues: 62.0856 Evaluate side-chains 50 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.094357 restraints weight = 3945.247| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.66 r_work: 0.2917 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3941 Z= 0.194 Angle : 0.568 6.834 5384 Z= 0.302 Chirality : 0.040 0.153 634 Planarity : 0.005 0.038 648 Dihedral : 9.377 69.582 591 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.01 % Allowed : 10.80 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.39), residues: 486 helix: 2.01 (0.27), residues: 360 sheet: -2.36 (1.47), residues: 10 loop : -1.06 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.002 0.001 HIS A 221 PHE 0.009 0.001 PHE A 488 TYR 0.012 0.001 TYR A 496 ARG 0.001 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.443 Fit side-chains REVERT: A 174 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7426 (mp) REVERT: A 263 SER cc_start: 0.7973 (m) cc_final: 0.7624 (p) REVERT: A 318 MET cc_start: 0.8181 (mtt) cc_final: 0.7833 (mtm) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 1.1285 time to fit residues: 58.6523 Evaluate side-chains 49 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.0070 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.095748 restraints weight = 3980.195| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.66 r_work: 0.2938 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3941 Z= 0.175 Angle : 0.538 6.053 5384 Z= 0.284 Chirality : 0.040 0.143 634 Planarity : 0.004 0.040 648 Dihedral : 6.228 37.558 591 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.01 % Allowed : 10.05 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.03 (0.39), residues: 486 helix: 2.18 (0.27), residues: 359 sheet: -2.25 (1.45), residues: 10 loop : -1.03 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 221 PHE 0.009 0.001 PHE A 488 TYR 0.012 0.001 TYR A 496 ARG 0.001 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.373 Fit side-chains REVERT: A 174 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 263 SER cc_start: 0.7984 (m) cc_final: 0.7695 (p) REVERT: A 318 MET cc_start: 0.8111 (mtt) cc_final: 0.7811 (mtm) outliers start: 8 outliers final: 2 residues processed: 52 average time/residue: 1.0780 time to fit residues: 58.2090 Evaluate side-chains 49 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4546 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.124282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097072 restraints weight = 4026.665| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.68 r_work: 0.2970 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3941 Z= 0.153 Angle : 0.506 6.056 5384 Z= 0.268 Chirality : 0.038 0.137 634 Planarity : 0.004 0.041 648 Dihedral : 4.923 34.811 591 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.76 % Allowed : 10.80 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.19 (0.39), residues: 486 helix: 2.30 (0.27), residues: 359 sheet: -2.08 (1.42), residues: 10 loop : -0.97 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.001 0.001 HIS A 221 PHE 0.009 0.001 PHE A 488 TYR 0.010 0.001 TYR A 496 ARG 0.001 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.374 Fit side-chains REVERT: A 174 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 263 SER cc_start: 0.7954 (m) cc_final: 0.7643 (p) REVERT: A 318 MET cc_start: 0.8117 (mtt) cc_final: 0.7873 (mtm) REVERT: A 400 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7627 (mtmm) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 1.0995 time to fit residues: 57.0871 Evaluate side-chains 49 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.122661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095353 restraints weight = 4061.453| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.69 r_work: 0.2934 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3941 Z= 0.182 Angle : 0.537 7.290 5384 Z= 0.285 Chirality : 0.039 0.150 634 Planarity : 0.004 0.045 648 Dihedral : 4.779 31.727 591 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.51 % Allowed : 11.06 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.11 (0.39), residues: 486 helix: 2.23 (0.27), residues: 359 sheet: -2.09 (1.45), residues: 10 loop : -0.97 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.001 0.001 HIS A 221 PHE 0.010 0.001 PHE A 502 TYR 0.012 0.001 TYR A 496 ARG 0.001 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.308 Fit side-chains REVERT: A 67 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 174 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 263 SER cc_start: 0.8048 (m) cc_final: 0.7746 (p) REVERT: A 318 MET cc_start: 0.8178 (mtt) cc_final: 0.7876 (mtm) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 1.0800 time to fit residues: 58.3000 Evaluate side-chains 51 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.122894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095617 restraints weight = 3999.449| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.68 r_work: 0.2936 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3941 Z= 0.176 Angle : 0.527 6.549 5384 Z= 0.281 Chirality : 0.039 0.148 634 Planarity : 0.005 0.063 648 Dihedral : 4.680 26.807 591 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.76 % Allowed : 11.56 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.12 (0.39), residues: 486 helix: 2.24 (0.27), residues: 359 sheet: -2.11 (1.45), residues: 10 loop : -0.97 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.001 0.000 HIS A 221 PHE 0.009 0.001 PHE A 502 TYR 0.012 0.001 TYR A 496 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.382 Fit side-chains REVERT: A 67 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: A 174 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 259 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 263 SER cc_start: 0.8015 (m) cc_final: 0.7692 (p) REVERT: A 318 MET cc_start: 0.8154 (mtt) cc_final: 0.7859 (mtm) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 1.0871 time to fit residues: 58.7204 Evaluate side-chains 50 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 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 = 0.3402 r_free = 0.3402 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095244 restraints weight = 3995.107| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.68 r_work: 0.2932 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3941 Z= 0.182 Angle : 0.535 6.499 5384 Z= 0.286 Chirality : 0.039 0.149 634 Planarity : 0.005 0.058 648 Dihedral : 4.653 28.949 591 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.51 % Allowed : 11.56 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.12 (0.39), residues: 486 helix: 2.22 (0.27), residues: 359 sheet: -2.09 (1.44), residues: 10 loop : -0.89 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.001 HIS A 221 PHE 0.010 0.001 PHE A 502 TYR 0.012 0.001 TYR A 496 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.334 Fit side-chains REVERT: A 67 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: A 174 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 259 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 263 SER cc_start: 0.8046 (m) cc_final: 0.7724 (p) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 1.1617 time to fit residues: 62.6383 Evaluate side-chains 52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.122543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095323 restraints weight = 3976.059| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.67 r_work: 0.2932 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3941 Z= 0.180 Angle : 0.538 6.334 5384 Z= 0.287 Chirality : 0.039 0.149 634 Planarity : 0.005 0.057 648 Dihedral : 4.652 30.712 591 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.76 % Allowed : 11.81 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.13 (0.39), residues: 486 helix: 2.23 (0.27), residues: 359 sheet: -2.06 (1.44), residues: 10 loop : -0.88 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.001 0.001 HIS A 221 PHE 0.010 0.001 PHE A 502 TYR 0.012 0.001 TYR A 496 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.394 Fit side-chains REVERT: A 67 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: A 174 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 259 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 263 SER cc_start: 0.8044 (m) cc_final: 0.7720 (p) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 1.1101 time to fit residues: 59.9324 Evaluate side-chains 52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 0.0010 overall best weight: 0.3964 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.125294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098153 restraints weight = 4004.926| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.68 r_work: 0.2988 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3941 Z= 0.147 Angle : 0.503 6.079 5384 Z= 0.266 Chirality : 0.038 0.135 634 Planarity : 0.004 0.052 648 Dihedral : 4.387 27.346 591 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.51 % Allowed : 12.56 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.33 (0.39), residues: 486 helix: 2.35 (0.27), residues: 360 sheet: -1.89 (1.49), residues: 10 loop : -0.77 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.001 0.000 HIS A 221 PHE 0.009 0.001 PHE A 488 TYR 0.009 0.001 TYR A 439 ARG 0.001 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.370 Fit side-chains REVERT: A 67 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: A 174 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7397 (mp) REVERT: A 259 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 263 SER cc_start: 0.7931 (m) cc_final: 0.7592 (p) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 1.0734 time to fit residues: 57.0031 Evaluate side-chains 53 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.121396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094021 restraints weight = 3981.733| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.68 r_work: 0.2913 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3941 Z= 0.202 Angle : 0.558 6.640 5384 Z= 0.299 Chirality : 0.040 0.156 634 Planarity : 0.005 0.067 648 Dihedral : 4.645 33.744 591 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.51 % Allowed : 12.31 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.11 (0.39), residues: 486 helix: 2.20 (0.27), residues: 359 sheet: -2.05 (1.39), residues: 10 loop : -0.86 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.002 0.001 HIS A 221 PHE 0.012 0.001 PHE A 502 TYR 0.013 0.001 TYR A 439 ARG 0.001 0.000 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.406 Fit side-chains REVERT: A 67 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: A 126 MET cc_start: 0.7333 (mmt) cc_final: 0.7129 (mmt) REVERT: A 174 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 259 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 263 SER cc_start: 0.8070 (m) cc_final: 0.7747 (p) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 1.0134 time to fit residues: 54.9821 Evaluate side-chains 54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.122647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095350 restraints weight = 3997.796| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.68 r_work: 0.2944 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3941 Z= 0.169 Angle : 0.526 6.026 5384 Z= 0.281 Chirality : 0.039 0.145 634 Planarity : 0.005 0.062 648 Dihedral : 4.560 33.505 591 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.51 % Allowed : 12.56 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.20 (0.39), residues: 486 helix: 2.27 (0.27), residues: 359 sheet: -1.91 (1.46), residues: 10 loop : -0.86 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.001 0.001 HIS A 221 PHE 0.009 0.001 PHE A 502 TYR 0.011 0.001 TYR A 496 ARG 0.001 0.000 ARG A 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.29 seconds wall clock time: 55 minutes 56.02 seconds (3356.02 seconds total)