Starting phenix.real_space_refine on Fri May 9 16:21:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrr_18624/05_2025/8qrr_18624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrr_18624/05_2025/8qrr_18624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrr_18624/05_2025/8qrr_18624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrr_18624/05_2025/8qrr_18624.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrr_18624/05_2025/8qrr_18624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrr_18624/05_2025/8qrr_18624.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2052 2.51 5 N 512 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3129 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3116 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 2.36, per 1000 atoms: 0.75 Number of scatterers: 3129 At special positions: 0 Unit cell: (60.192, 70.224, 75.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 Na 3 11.00 O 546 8.00 N 512 7.00 C 2052 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: 0.74 Conformation dependent library (CDL) restraints added in 363.6 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 85.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 52 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.687A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.795A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 249 through 292 removed outlier: 4.530A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.731A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 383 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 4.110A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.522A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.640A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 260 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.88 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: 988 1.34 - 1.46: 426 1.46 - 1.57: 1742 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3181 Sorted by residual: bond pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.19e-01 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.51e-01 bond pdb=" CG LEU B 107 " pdb=" CD1 LEU B 107 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" CG1 ILE B 104 " pdb=" CD1 ILE B 104 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.35e-01 bond pdb=" CA VAL B 472 " pdb=" C VAL B 472 " ideal model delta sigma weight residual 1.523 1.516 0.007 1.27e-02 6.20e+03 3.31e-01 ... (remaining 3176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 4214 1.12 - 2.23: 80 2.23 - 3.35: 23 3.35 - 4.47: 8 4.47 - 5.58: 7 Bond angle restraints: 4332 Sorted by residual: angle pdb=" CB ARG B 301 " pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.89e+00 angle pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " pdb=" NE ARG B 301 " ideal model delta sigma weight residual 112.00 117.10 -5.10 2.20e+00 2.07e-01 5.37e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 114.29 -3.89 1.70e+00 3.46e-01 5.25e+00 angle pdb=" N ILE B 103 " pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 109.34 113.04 -3.70 2.08e+00 2.31e-01 3.16e+00 angle pdb=" N VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 112.16 110.10 2.06 1.30e+00 5.92e-01 2.51e+00 ... (remaining 4327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1669 17.95 - 35.89: 166 35.89 - 53.83: 28 53.83 - 71.78: 1 71.78 - 89.72: 3 Dihedral angle restraints: 1867 sinusoidal: 681 harmonic: 1186 Sorted by residual: dihedral pdb=" CA ASP B 294 " pdb=" CB ASP B 294 " pdb=" CG ASP B 294 " pdb=" OD1 ASP B 294 " ideal model delta sinusoidal sigma weight residual -30.00 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " pdb=" OE1 GLU B 251 " ideal model delta sinusoidal sigma weight residual 0.00 85.67 -85.67 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -130.28 -49.72 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 1864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 468 0.059 - 0.118: 73 0.118 - 0.177: 1 0.177 - 0.235: 0 0.235 - 0.294: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 540 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 474 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLY B 474 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY B 474 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B 475 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 471 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN B 471 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 471 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 472 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 469 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL B 469 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 469 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 470 " -0.009 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 617 2.77 - 3.30: 3207 3.30 - 3.83: 5511 3.83 - 4.37: 6085 4.37 - 4.90: 11075 Nonbonded interactions: 26495 Sorted by model distance: nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.234 2.470 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.255 2.470 nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.278 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.288 2.470 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.310 2.470 ... (remaining 26490 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: 0.570 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 0.029 3181 Z= 0.122 Angle : 0.491 5.583 4332 Z= 0.255 Chirality : 0.039 0.294 543 Planarity : 0.005 0.055 536 Dihedral : 14.324 89.721 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.21 % Allowed : 18.48 % Favored : 80.30 % 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: 2.25 (0.43), residues: 414 helix: 1.96 (0.29), residues: 340 sheet: -1.40 (1.27), residues: 20 loop : -0.25 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.001 0.001 HIS B 452 PHE 0.008 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.12153 ( 260) hydrogen bonds : angle 5.95125 ( 780) covalent geometry : bond 0.00264 ( 3181) covalent geometry : angle 0.49072 ( 4332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.320 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.9557 time to fit residues: 44.6368 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 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 = 0.3574 r_free = 0.3574 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094484 restraints weight = 3645.211| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.96 r_work: 0.2951 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.137 Angle : 0.510 6.133 4332 Z= 0.255 Chirality : 0.039 0.199 543 Planarity : 0.004 0.030 536 Dihedral : 3.771 29.938 446 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.03 % Allowed : 17.27 % Favored : 79.70 % 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: 2.93 (0.43), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: -1.37 (1.28), residues: 20 loop : 0.01 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.008 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 260) hydrogen bonds : angle 4.52931 ( 780) covalent geometry : bond 0.00308 ( 3181) covalent geometry : angle 0.50975 ( 4332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.306 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.8732 time to fit residues: 46.3208 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093083 restraints weight = 3595.173| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.94 r_work: 0.2931 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3181 Z= 0.150 Angle : 0.511 5.252 4332 Z= 0.256 Chirality : 0.040 0.243 543 Planarity : 0.004 0.031 536 Dihedral : 3.262 13.494 441 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.15 % Allowed : 15.45 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.90 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.001 TYR B 334 ARG 0.008 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 260) hydrogen bonds : angle 4.46819 ( 780) covalent geometry : bond 0.00353 ( 3181) covalent geometry : angle 0.51073 ( 4332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.359 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 51 average time/residue: 0.8712 time to fit residues: 46.2490 Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092944 restraints weight = 3695.761| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.97 r_work: 0.2928 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3181 Z= 0.144 Angle : 0.508 5.177 4332 Z= 0.254 Chirality : 0.040 0.258 543 Planarity : 0.004 0.031 536 Dihedral : 3.268 13.619 441 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.24 % Allowed : 15.76 % Favored : 80.00 % 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: 2.84 (0.42), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.90 (0.69), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 HIS 0.001 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.001 TYR B 334 ARG 0.010 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 260) hydrogen bonds : angle 4.42848 ( 780) covalent geometry : bond 0.00338 ( 3181) covalent geometry : angle 0.50779 ( 4332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.322 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 47 average time/residue: 0.8514 time to fit residues: 41.7300 Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.130311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095501 restraints weight = 3654.244| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.97 r_work: 0.2966 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.120 Angle : 0.489 5.423 4332 Z= 0.243 Chirality : 0.039 0.275 543 Planarity : 0.004 0.034 536 Dihedral : 3.190 11.812 441 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.64 % Allowed : 16.36 % Favored : 80.00 % 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: 2.97 (0.42), residues: 414 helix: 2.52 (0.28), residues: 341 sheet: -1.40 (1.28), residues: 20 loop : -0.38 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.012 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 260) hydrogen bonds : angle 4.32380 ( 780) covalent geometry : bond 0.00268 ( 3181) covalent geometry : angle 0.48865 ( 4332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.331 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 49 average time/residue: 0.8323 time to fit residues: 42.4870 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 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 = 0.3564 r_free = 0.3564 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093277 restraints weight = 3754.875| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.00 r_work: 0.2936 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3181 Z= 0.144 Angle : 0.529 8.288 4332 Z= 0.258 Chirality : 0.040 0.282 543 Planarity : 0.004 0.037 536 Dihedral : 3.234 12.494 441 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.55 % Allowed : 15.76 % Favored : 79.70 % 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: 2.86 (0.42), residues: 414 helix: 2.46 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.00 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 338 HIS 0.002 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.002 TYR B 334 ARG 0.012 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 260) hydrogen bonds : angle 4.37672 ( 780) covalent geometry : bond 0.00341 ( 3181) covalent geometry : angle 0.52947 ( 4332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.318 Fit side-chains REVERT: B 292 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6490 (mpt) outliers start: 15 outliers final: 4 residues processed: 49 average time/residue: 0.8843 time to fit residues: 45.0719 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094625 restraints weight = 3632.577| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.97 r_work: 0.2959 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3181 Z= 0.131 Angle : 0.527 7.442 4332 Z= 0.256 Chirality : 0.040 0.296 543 Planarity : 0.004 0.041 536 Dihedral : 3.238 12.785 441 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.33 % Allowed : 16.97 % Favored : 79.70 % 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: 2.93 (0.42), residues: 414 helix: 2.52 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.04 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.013 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 260) hydrogen bonds : angle 4.34394 ( 780) covalent geometry : bond 0.00302 ( 3181) covalent geometry : angle 0.52679 ( 4332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.315 Fit side-chains REVERT: B 292 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6509 (mpt) outliers start: 11 outliers final: 4 residues processed: 45 average time/residue: 0.9507 time to fit residues: 44.4621 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094834 restraints weight = 3668.345| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.97 r_work: 0.2962 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.130 Angle : 0.523 7.143 4332 Z= 0.255 Chirality : 0.040 0.303 543 Planarity : 0.004 0.044 536 Dihedral : 3.225 12.829 441 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.73 % Allowed : 17.58 % Favored : 79.70 % 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: 2.92 (0.42), residues: 414 helix: 2.52 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.02 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.013 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 260) hydrogen bonds : angle 4.33417 ( 780) covalent geometry : bond 0.00299 ( 3181) covalent geometry : angle 0.52288 ( 4332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.373 Fit side-chains REVERT: B 292 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6500 (mpt) outliers start: 9 outliers final: 3 residues processed: 45 average time/residue: 0.9518 time to fit residues: 44.6068 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095845 restraints weight = 3681.656| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.98 r_work: 0.2974 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3181 Z= 0.123 Angle : 0.523 6.981 4332 Z= 0.254 Chirality : 0.040 0.309 543 Planarity : 0.004 0.048 536 Dihedral : 3.219 12.192 441 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.73 % Allowed : 17.58 % Favored : 79.70 % 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: 3.02 (0.42), residues: 414 helix: 2.56 (0.28), residues: 341 sheet: -1.61 (1.29), residues: 20 loop : -0.39 (0.84), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 260) hydrogen bonds : angle 4.29958 ( 780) covalent geometry : bond 0.00280 ( 3181) covalent geometry : angle 0.52297 ( 4332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.345 Fit side-chains REVERT: B 292 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6519 (mpt) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 1.0173 time to fit residues: 47.4728 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095434 restraints weight = 3625.013| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.03 r_work: 0.2973 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3181 Z= 0.122 Angle : 0.526 6.907 4332 Z= 0.255 Chirality : 0.040 0.304 543 Planarity : 0.004 0.050 536 Dihedral : 3.218 12.142 441 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.82 % Allowed : 19.09 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.43), residues: 414 helix: 2.58 (0.28), residues: 341 sheet: -1.61 (1.29), residues: 20 loop : -0.39 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.015 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 260) hydrogen bonds : angle 4.28651 ( 780) covalent geometry : bond 0.00277 ( 3181) covalent geometry : angle 0.52581 ( 4332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.358 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.9023 time to fit residues: 42.1435 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 chunk 15 optimal weight: 2.9990 overall best weight: 0.5628 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.130621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095649 restraints weight = 3680.070| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.98 r_work: 0.2977 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3181 Z= 0.125 Angle : 0.527 6.814 4332 Z= 0.255 Chirality : 0.040 0.298 543 Planarity : 0.004 0.050 536 Dihedral : 3.213 12.059 441 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.21 % Allowed : 19.39 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.42), residues: 414 helix: 2.59 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.015 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 260) hydrogen bonds : angle 4.29846 ( 780) covalent geometry : bond 0.00284 ( 3181) covalent geometry : angle 0.52685 ( 4332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.39 seconds wall clock time: 44 minutes 33.79 seconds (2673.79 seconds total)