Starting phenix.real_space_refine on Mon Feb 10 21:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z80_39834/02_2025/8z80_39834.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z80_39834/02_2025/8z80_39834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z80_39834/02_2025/8z80_39834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z80_39834/02_2025/8z80_39834.map" model { file = "/net/cci-nas-00/data/ceres_data/8z80_39834/02_2025/8z80_39834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z80_39834/02_2025/8z80_39834.cif" } resolution = 3.7 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= 0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 1882 2.51 5 N 433 2.21 5 O 502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2828 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2816 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UEG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 1.01 Number of scatterers: 2828 At special positions: 0 Unit cell: (78.288, 68.968, 68.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 502 8.00 N 433 7.00 C 1882 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: 0.80 Conformation dependent library (CDL) restraints added in 396.2 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.724A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 95 removed outlier: 4.788A pdb=" N TYR B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Proline residue: B 75 - end of helix removed outlier: 4.483A pdb=" N PHE B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Proline residue: B 87 - end of helix removed outlier: 3.893A pdb=" N ASP B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.903A pdb=" N ILE B 145 " --> pdb=" O TYR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 150 through 181 removed outlier: 4.055A pdb=" N GLN B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 206 removed outlier: 3.729A pdb=" N LEU B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.655A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N CYS B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 297' Processing helix chain 'B' and resid 298 through 324 removed outlier: 4.658A pdb=" N ASN B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 3.704A pdb=" N VAL B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 382 Processing helix chain 'B' and resid 386 through 415 Processing helix chain 'B' and resid 419 through 442 removed outlier: 3.589A pdb=" N THR B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.074A pdb=" N PHE B 456 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 457 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 482 removed outlier: 3.673A pdb=" N ILE B 466 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N CYS B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 675 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: 0.77 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 519 1.33 - 1.45: 745 1.45 - 1.57: 1615 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2895 Sorted by residual: bond pdb=" C3 UEG B 501 " pdb=" O3 UEG B 501 " ideal model delta sigma weight residual 1.348 1.481 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C2 UEG B 501 " pdb=" C2A UEG B 501 " ideal model delta sigma weight residual 1.500 1.561 -0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" C5 UEG B 501 " pdb=" C6 UEG B 501 " ideal model delta sigma weight residual 1.388 1.339 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C4 UEG B 501 " pdb=" C4A UEG B 501 " ideal model delta sigma weight residual 1.504 1.553 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C5 UEG B 501 " pdb=" C5A UEG B 501 " ideal model delta sigma weight residual 1.505 1.552 -0.047 2.00e-02 2.50e+03 5.44e+00 ... (remaining 2890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3825 1.63 - 3.26: 119 3.26 - 4.89: 27 4.89 - 6.52: 7 6.52 - 8.15: 5 Bond angle restraints: 3983 Sorted by residual: angle pdb=" N GLN B 435 " pdb=" CA GLN B 435 " pdb=" CB GLN B 435 " ideal model delta sigma weight residual 110.12 115.47 -5.35 1.47e+00 4.63e-01 1.33e+01 angle pdb=" C CYS B 297 " pdb=" N TRP B 298 " pdb=" CA TRP B 298 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA GLN B 435 " pdb=" CB GLN B 435 " pdb=" CG GLN B 435 " ideal model delta sigma weight residual 114.10 119.59 -5.49 2.00e+00 2.50e-01 7.53e+00 angle pdb=" C ARG B 96 " pdb=" N TYR B 97 " pdb=" CA TYR B 97 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.41e+00 angle pdb=" N TYR B 74 " pdb=" CA TYR B 74 " pdb=" C TYR B 74 " ideal model delta sigma weight residual 109.81 115.17 -5.36 2.21e+00 2.05e-01 5.87e+00 ... (remaining 3978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 1489 16.64 - 33.28: 128 33.28 - 49.92: 18 49.92 - 66.56: 1 66.56 - 83.20: 3 Dihedral angle restraints: 1639 sinusoidal: 496 harmonic: 1143 Sorted by residual: dihedral pdb=" CA VAL B 442 " pdb=" C VAL B 442 " pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta harmonic sigma weight residual -180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA ASP B 381 " pdb=" C ASP B 381 " pdb=" N THR B 382 " pdb=" CA THR B 382 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU B 321 " pdb=" CG GLU B 321 " pdb=" CD GLU B 321 " pdb=" OE1 GLU B 321 " ideal model delta sinusoidal sigma weight residual 0.00 -83.20 83.20 1 3.00e+01 1.11e-03 9.40e+00 ... (remaining 1636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 372 0.047 - 0.094: 105 0.094 - 0.140: 17 0.140 - 0.187: 1 0.187 - 0.233: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB ILE B 386 " pdb=" CA ILE B 386 " pdb=" CG1 ILE B 386 " pdb=" CG2 ILE B 386 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA THR B 54 " pdb=" N THR B 54 " pdb=" C THR B 54 " pdb=" CB THR B 54 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 494 not shown) Planarity restraints: 483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 59 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 60 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 32 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 33 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 298 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C TRP B 298 " -0.031 2.00e-02 2.50e+03 pdb=" O TRP B 298 " 0.011 2.00e-02 2.50e+03 pdb=" N SER B 299 " 0.010 2.00e-02 2.50e+03 ... (remaining 480 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 689 2.78 - 3.31: 3000 3.31 - 3.84: 4826 3.84 - 4.37: 5031 4.37 - 4.90: 8826 Nonbonded interactions: 22372 Sorted by model distance: nonbonded pdb=" OH TYR B 40 " pdb=" OE1 GLN B 104 " model vdw 2.251 3.040 nonbonded pdb=" O PHE B 89 " pdb=" OG1 THR B 92 " model vdw 2.271 3.040 nonbonded pdb=" NE2 GLN B 311 " pdb=" OH TYR B 459 " model vdw 2.295 3.120 nonbonded pdb=" O MET B 401 " pdb=" OG1 THR B 405 " model vdw 2.296 3.040 nonbonded pdb=" OG SER B 370 " pdb=" O PHE B 463 " model vdw 2.325 3.040 ... (remaining 22367 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 : 0.004 0.133 2895 Z= 0.288 Angle : 0.741 8.147 3983 Z= 0.384 Chirality : 0.044 0.233 497 Planarity : 0.006 0.071 483 Dihedral : 13.051 83.196 905 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.42), residues: 385 helix: 1.03 (0.31), residues: 277 sheet: None (None), residues: 0 loop : -1.03 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 298 PHE 0.031 0.002 PHE B 409 TYR 0.029 0.002 TYR B 390 ARG 0.012 0.002 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.261 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1076 time to fit residues: 10.7060 Evaluate side-chains 66 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.212628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.199226 restraints weight = 6612.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.202232 restraints weight = 4335.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.204482 restraints weight = 3073.894| |-----------------------------------------------------------------------------| r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2895 Z= 0.168 Angle : 0.605 9.266 3983 Z= 0.317 Chirality : 0.040 0.179 497 Planarity : 0.005 0.058 483 Dihedral : 4.667 29.105 416 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.53 % Allowed : 11.83 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.42), residues: 385 helix: 0.92 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.18 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 298 PHE 0.020 0.001 PHE B 409 TYR 0.023 0.002 TYR B 400 ARG 0.005 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 128 GLU cc_start: 0.7396 (tp30) cc_final: 0.6798 (tp30) REVERT: B 309 TYR cc_start: 0.6698 (t80) cc_final: 0.6464 (t80) REVERT: B 380 MET cc_start: 0.6582 (ptt) cc_final: 0.6370 (ptt) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1076 time to fit residues: 10.1240 Evaluate side-chains 72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 298 TRP Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 GLN B 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.207854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.194578 restraints weight = 6638.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.197494 restraints weight = 4337.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.199654 restraints weight = 3042.434| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2895 Z= 0.229 Angle : 0.661 9.767 3983 Z= 0.344 Chirality : 0.042 0.181 497 Planarity : 0.005 0.055 483 Dihedral : 5.043 31.130 416 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.05 % Allowed : 18.32 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.42), residues: 385 helix: 0.60 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -1.27 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 112 PHE 0.018 0.002 PHE B 409 TYR 0.034 0.002 TYR B 400 ARG 0.004 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: B 112 TRP cc_start: 0.6247 (m100) cc_final: 0.5897 (m100) REVERT: B 309 TYR cc_start: 0.6800 (t80) cc_final: 0.6494 (t80) REVERT: B 400 TYR cc_start: 0.7917 (t80) cc_final: 0.7578 (t80) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.1083 time to fit residues: 10.5033 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.208703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.194544 restraints weight = 6730.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.197600 restraints weight = 4379.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.199742 restraints weight = 3060.614| |-----------------------------------------------------------------------------| r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2895 Z= 0.179 Angle : 0.608 9.635 3983 Z= 0.314 Chirality : 0.040 0.180 497 Planarity : 0.005 0.054 483 Dihedral : 4.823 30.178 416 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.58 % Allowed : 22.14 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.42), residues: 385 helix: 0.74 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -1.32 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 112 PHE 0.011 0.001 PHE B 42 TYR 0.026 0.002 TYR B 79 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.250 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.1196 time to fit residues: 12.1749 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 3 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.209567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.195827 restraints weight = 6629.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.198803 restraints weight = 4199.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.200903 restraints weight = 2930.407| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2895 Z= 0.177 Angle : 0.601 9.570 3983 Z= 0.316 Chirality : 0.040 0.172 497 Planarity : 0.005 0.049 483 Dihedral : 4.758 30.632 416 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.44 % Allowed : 24.43 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.42), residues: 385 helix: 0.86 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -1.33 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 112 PHE 0.019 0.001 PHE B 409 TYR 0.041 0.002 TYR B 400 ARG 0.002 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7602 (pm20) cc_final: 0.7332 (pm20) REVERT: B 309 TYR cc_start: 0.6818 (t80) cc_final: 0.6316 (t80) REVERT: B 400 TYR cc_start: 0.7940 (t80) cc_final: 0.7642 (t80) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.1136 time to fit residues: 11.2988 Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 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 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.208661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.194683 restraints weight = 6722.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.197677 restraints weight = 4263.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.199709 restraints weight = 2955.789| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2895 Z= 0.201 Angle : 0.625 9.709 3983 Z= 0.322 Chirality : 0.040 0.174 497 Planarity : 0.005 0.046 483 Dihedral : 4.657 27.657 416 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.96 % Allowed : 24.43 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.43), residues: 385 helix: 0.87 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.52 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 112 PHE 0.010 0.001 PHE B 409 TYR 0.032 0.002 TYR B 400 ARG 0.002 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 309 TYR cc_start: 0.6976 (t80) cc_final: 0.6742 (t80) REVERT: B 402 LEU cc_start: 0.8429 (mm) cc_final: 0.8227 (mm) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.1068 time to fit residues: 11.0716 Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4629 r_free = 0.4629 target = 0.208910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.194913 restraints weight = 6847.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.197887 restraints weight = 4321.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.199967 restraints weight = 3006.616| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 2895 Z= 0.213 Angle : 0.648 10.996 3983 Z= 0.334 Chirality : 0.041 0.173 497 Planarity : 0.005 0.045 483 Dihedral : 4.554 24.759 416 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.67 % Allowed : 26.34 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.43), residues: 385 helix: 0.88 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.56 (0.64), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 302 PHE 0.024 0.001 PHE B 409 TYR 0.045 0.002 TYR B 400 ARG 0.002 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 309 TYR cc_start: 0.7025 (t80) cc_final: 0.6595 (t80) outliers start: 7 outliers final: 7 residues processed: 79 average time/residue: 0.1079 time to fit residues: 10.8205 Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4616 r_free = 0.4616 target = 0.208207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.194212 restraints weight = 6556.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.197208 restraints weight = 4214.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.199093 restraints weight = 2935.662| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 2895 Z= 0.204 Angle : 0.649 11.512 3983 Z= 0.333 Chirality : 0.041 0.179 497 Planarity : 0.005 0.043 483 Dihedral : 4.477 20.975 416 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.44 % Allowed : 25.95 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.43), residues: 385 helix: 0.87 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.54 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 302 PHE 0.012 0.001 PHE B 409 TYR 0.046 0.002 TYR B 400 ARG 0.003 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6761 (pp20) cc_final: 0.6535 (pp20) REVERT: B 309 TYR cc_start: 0.6854 (t80) cc_final: 0.6484 (t80) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.1136 time to fit residues: 11.3099 Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.0870 chunk 26 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.209634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.195884 restraints weight = 6569.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.198827 restraints weight = 4209.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.200957 restraints weight = 2925.318| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2895 Z= 0.186 Angle : 0.631 11.056 3983 Z= 0.323 Chirality : 0.040 0.171 497 Planarity : 0.004 0.043 483 Dihedral : 4.258 22.177 416 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.05 % Allowed : 27.10 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.43), residues: 385 helix: 1.02 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.44 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 302 PHE 0.008 0.001 PHE B 42 TYR 0.040 0.002 TYR B 400 ARG 0.002 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6654 (pp20) cc_final: 0.6444 (pp20) REVERT: B 309 TYR cc_start: 0.6860 (t80) cc_final: 0.6521 (t80) outliers start: 8 outliers final: 8 residues processed: 82 average time/residue: 0.1055 time to fit residues: 11.0488 Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.210681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.196563 restraints weight = 6650.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.199598 restraints weight = 4218.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.201768 restraints weight = 2927.353| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 2895 Z= 0.178 Angle : 0.657 11.524 3983 Z= 0.333 Chirality : 0.040 0.175 497 Planarity : 0.004 0.043 483 Dihedral : 4.139 24.669 416 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 27.10 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.42), residues: 385 helix: 1.05 (0.30), residues: 299 sheet: None (None), residues: 0 loop : -1.66 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 302 PHE 0.007 0.001 PHE B 42 TYR 0.043 0.002 TYR B 400 ARG 0.002 0.000 ARG B 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6775 (pp20) cc_final: 0.6569 (pp20) REVERT: B 162 ARG cc_start: 0.7274 (mtm180) cc_final: 0.6979 (ptt-90) REVERT: B 309 TYR cc_start: 0.6790 (t80) cc_final: 0.6429 (t80) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.1132 time to fit residues: 10.8730 Evaluate side-chains 75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.210451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.196515 restraints weight = 6542.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.199446 restraints weight = 4233.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.201612 restraints weight = 2981.393| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2895 Z= 0.194 Angle : 0.662 11.374 3983 Z= 0.335 Chirality : 0.040 0.172 497 Planarity : 0.005 0.042 483 Dihedral : 4.172 23.686 416 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.29 % Allowed : 28.63 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.42), residues: 385 helix: 1.08 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.56 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 112 PHE 0.008 0.001 PHE B 42 TYR 0.037 0.002 TYR B 400 ARG 0.002 0.000 ARG B 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.13 seconds wall clock time: 23 minutes 31.34 seconds (1411.34 seconds total)