Starting phenix.real_space_refine on Wed Mar 5 16:38:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z80_39834/03_2025/8z80_39834.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z80_39834/03_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_39834/03_2025/8z80_39834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z80_39834/03_2025/8z80_39834.map" model { file = "/net/cci-nas-00/data/ceres_data/8z80_39834/03_2025/8z80_39834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z80_39834/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.93, per 1000 atoms: 1.04 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: 0.99 Conformation dependent library (CDL) restraints added in 347.8 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: 0.28 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: 0.88 Time building geometry restraints manager: 0.85 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: 1.110 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: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- 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 : 0.273 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1097 time to fit residues: 10.9256 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 : 0.302 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.199217 restraints weight = 6612.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.202179 restraints weight = 4347.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.204384 restraints weight = 3088.817| |-----------------------------------------------------------------------------| r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 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 29.104 416 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 : 0.265 Fit side-chains revert: symmetry clash REVERT: B 128 GLU cc_start: 0.7414 (tp30) cc_final: 0.6804 (tp30) REVERT: B 309 TYR cc_start: 0.6718 (t80) cc_final: 0.6484 (t80) REVERT: B 380 MET cc_start: 0.6561 (ptt) cc_final: 0.6351 (ptt) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1018 time to fit residues: 9.6254 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 : 0.266 ------------------------------------------------------------------------------- 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: 0.7980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4649 r_free = 0.4649 target = 0.210854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.197536 restraints weight = 6632.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.200471 restraints weight = 4304.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.202583 restraints weight = 3040.120| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2895 Z= 0.186 Angle : 0.602 9.496 3983 Z= 0.315 Chirality : 0.040 0.184 497 Planarity : 0.005 0.055 483 Dihedral : 4.674 26.813 416 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.67 % Allowed : 17.94 % 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: 0.48 (0.42), residues: 385 helix: 0.86 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -1.30 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 112 PHE 0.018 0.001 PHE B 409 TYR 0.035 0.002 TYR B 400 ARG 0.003 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 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 309 TYR cc_start: 0.6728 (t80) cc_final: 0.6402 (t80) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.1062 time to fit residues: 10.1494 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4619 r_free = 0.4619 target = 0.207855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.194097 restraints weight = 6673.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.197058 restraints weight = 4266.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.199234 restraints weight = 2989.783| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2895 Z= 0.210 Angle : 0.636 9.663 3983 Z= 0.329 Chirality : 0.041 0.178 497 Planarity : 0.005 0.052 483 Dihedral : 4.847 28.577 416 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.82 % Allowed : 21.37 % Favored : 74.81 % 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: 0.38 (0.42), residues: 385 helix: 0.79 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -1.33 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 112 PHE 0.011 0.001 PHE B 42 TYR 0.046 0.003 TYR B 400 ARG 0.002 0.001 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 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 309 TYR cc_start: 0.6848 (t80) cc_final: 0.6450 (t80) REVERT: B 400 TYR cc_start: 0.7883 (t80) cc_final: 0.7660 (t80) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.1086 time to fit residues: 10.8753 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 : 0.294 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.208500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.194943 restraints weight = 6558.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.197846 restraints weight = 4132.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.200013 restraints weight = 2864.561| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2895 Z= 0.194 Angle : 0.607 9.576 3983 Z= 0.318 Chirality : 0.040 0.174 497 Planarity : 0.005 0.048 483 Dihedral : 4.809 31.396 416 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.82 % Allowed : 23.28 % Favored : 72.90 % 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 (0.43), residues: 385 helix: 0.86 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -1.34 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 112 PHE 0.020 0.001 PHE B 409 TYR 0.031 0.002 TYR B 400 ARG 0.002 0.000 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: 10 poor density : 71 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7586 (pm20) cc_final: 0.7312 (pm20) REVERT: B 309 TYR cc_start: 0.6929 (t80) cc_final: 0.6697 (t80) REVERT: B 400 TYR cc_start: 0.7997 (t80) cc_final: 0.7780 (t80) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.1122 time to fit residues: 11.0201 Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 333 ASN 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: 0.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4624 r_free = 0.4624 target = 0.208585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.194913 restraints weight = 6708.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.197777 restraints weight = 4195.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.199893 restraints weight = 2923.844| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2895 Z= 0.201 Angle : 0.622 9.618 3983 Z= 0.323 Chirality : 0.040 0.174 497 Planarity : 0.005 0.046 483 Dihedral : 4.739 29.538 416 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.58 % Allowed : 24.81 % 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: 0.86 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.50 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 112 PHE 0.010 0.001 PHE B 42 TYR 0.026 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: 12 poor density : 75 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1059 time to fit residues: 11.1843 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 89 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.209277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.195309 restraints weight = 6815.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.198323 restraints weight = 4345.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.200492 restraints weight = 3014.996| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2895 Z= 0.192 Angle : 0.653 12.638 3983 Z= 0.329 Chirality : 0.041 0.194 497 Planarity : 0.005 0.045 483 Dihedral : 4.554 25.772 416 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.82 % Allowed : 24.43 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.43), residues: 385 helix: 0.89 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.48 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 112 PHE 0.024 0.001 PHE B 409 TYR 0.042 0.002 TYR B 400 ARG 0.002 0.001 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 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 309 TYR cc_start: 0.6544 (t80) cc_final: 0.5996 (t80) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.1037 time to fit residues: 10.6661 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 LEU 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 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: 0.9980 chunk 36 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 18 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4631 r_free = 0.4631 target = 0.209335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.195471 restraints weight = 6579.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.198416 restraints weight = 4221.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.200546 restraints weight = 2946.859| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 2895 Z= 0.195 Angle : 0.646 9.835 3983 Z= 0.334 Chirality : 0.041 0.172 497 Planarity : 0.005 0.043 483 Dihedral : 4.401 21.469 416 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.44 % Allowed : 25.57 % 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: 0.62 (0.43), residues: 385 helix: 1.00 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.50 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 302 PHE 0.011 0.001 PHE B 409 TYR 0.040 0.002 TYR B 400 ARG 0.008 0.001 ARG B 397 *********************** 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 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6747 (pp20) cc_final: 0.6468 (pp20) REVERT: B 309 TYR cc_start: 0.6746 (t80) cc_final: 0.6025 (t80) outliers start: 9 outliers final: 9 residues processed: 79 average time/residue: 0.1032 time to fit residues: 10.4055 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.3980 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.208639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.194968 restraints weight = 6586.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.197919 restraints weight = 4161.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.200060 restraints weight = 2880.760| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 2895 Z= 0.201 Angle : 0.666 9.883 3983 Z= 0.340 Chirality : 0.041 0.173 497 Planarity : 0.005 0.043 483 Dihedral : 4.375 18.946 416 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.05 % Allowed : 26.34 % 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: 0.61 (0.42), residues: 385 helix: 1.00 (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 0.017 0.001 TRP B 302 PHE 0.010 0.001 PHE B 42 TYR 0.038 0.002 TYR B 400 ARG 0.006 0.001 ARG B 397 *********************** 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 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6769 (pp20) cc_final: 0.6550 (pp20) REVERT: B 400 TYR cc_start: 0.7898 (t80) cc_final: 0.7660 (t80) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.1097 time to fit residues: 10.9278 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 LEU 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 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 9 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.210125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.196283 restraints weight = 6647.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.199254 restraints weight = 4218.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.201432 restraints weight = 2917.326| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 2895 Z= 0.189 Angle : 0.659 10.336 3983 Z= 0.335 Chirality : 0.041 0.175 497 Planarity : 0.005 0.042 483 Dihedral : 4.210 19.427 416 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.05 % Allowed : 26.72 % Favored : 70.23 % 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: 0.71 (0.42), residues: 385 helix: 1.06 (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 0.002 TRP B 302 PHE 0.008 0.001 PHE B 42 TYR 0.036 0.002 TYR B 400 ARG 0.005 0.001 ARG B 397 ********************** 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 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6748 (pp20) cc_final: 0.6535 (pp20) REVERT: B 162 ARG cc_start: 0.7241 (mtm180) cc_final: 0.6960 (ptt-90) REVERT: B 309 TYR cc_start: 0.6092 (t80) cc_final: 0.5423 (t80) REVERT: B 321 GLU cc_start: 0.6290 (tp30) cc_final: 0.5624 (tp30) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.1033 time to fit residues: 10.2514 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 LEU 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 446 SER 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: 3.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.0000 overall best weight: 0.3902 ------------------------------------------------------------------------------- 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 = 0.210531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.196152 restraints weight = 6548.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.199164 restraints weight = 4333.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.201359 restraints weight = 3036.718| |-----------------------------------------------------------------------------| r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3137 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= 0.182 Angle : 0.662 10.095 3983 Z= 0.333 Chirality : 0.040 0.173 497 Planarity : 0.005 0.042 483 Dihedral : 4.134 20.654 416 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 28.24 % 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: 0.72 (0.42), residues: 385 helix: 1.10 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.55 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 302 PHE 0.008 0.001 PHE B 42 TYR 0.032 0.002 TYR B 309 ARG 0.003 0.001 ARG B 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.37 seconds wall clock time: 23 minutes 41.34 seconds (1421.34 seconds total)