Starting phenix.real_space_refine on Wed Mar 5 18:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtg_32785/03_2025/7wtg_32785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtg_32785/03_2025/7wtg_32785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2025/7wtg_32785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2025/7wtg_32785.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2025/7wtg_32785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2025/7wtg_32785.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 17 5.16 5 C 2107 2.51 5 N 563 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3318 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Time building chain proxies: 3.50, per 1000 atoms: 1.05 Number of scatterers: 3318 At special positions: 0 Unit cell: (60.32, 64.48, 115.44, 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 17 16.00 O 631 8.00 N 563 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 0.70 Conformation dependent library (CDL) restraints added in 898.1 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 5.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.596A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.762A pdb=" N ILE E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 406 through 411' Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.408A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.513A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU H 99 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 180 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: 0.75 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1064 1.35 - 1.47: 930 1.47 - 1.60: 1389 1.60 - 1.73: 0 1.73 - 1.85: 21 Bond restraints: 3404 Sorted by residual: bond pdb=" N VAL E 445 " pdb=" CA VAL E 445 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.77e+00 bond pdb=" N LYS E 444 " pdb=" CA LYS E 444 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.14e+00 bond pdb=" N GLY E 447 " pdb=" CA GLY E 447 " ideal model delta sigma weight residual 1.450 1.476 -0.025 1.01e-02 9.80e+03 6.18e+00 bond pdb=" N SER E 446 " pdb=" CA SER E 446 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.66e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 4.06e+00 ... (remaining 3399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 4350 2.34 - 4.68: 212 4.68 - 7.03: 43 7.03 - 9.37: 13 9.37 - 11.71: 2 Bond angle restraints: 4620 Sorted by residual: angle pdb=" C ILE E 410 " pdb=" N ALA E 411 " pdb=" CA ALA E 411 " ideal model delta sigma weight residual 120.60 127.40 -6.80 1.53e+00 4.27e-01 1.98e+01 angle pdb=" C GLY H 113 " pdb=" N MET H 114 " pdb=" CA MET H 114 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.77e+01 angle pdb=" CA GLY E 447 " pdb=" C GLY E 447 " pdb=" O GLY E 447 " ideal model delta sigma weight residual 122.05 118.00 4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" C GLN H 62 " pdb=" N LYS H 63 " pdb=" CA LYS H 63 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1798 17.95 - 35.90: 181 35.90 - 53.84: 29 53.84 - 71.79: 4 71.79 - 89.74: 5 Dihedral angle restraints: 2017 sinusoidal: 790 harmonic: 1227 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.13 -72.13 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PRO E 337 " pdb=" C PRO E 337 " pdb=" N PHE E 338 " pdb=" CA PHE E 338 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 349 0.058 - 0.116: 95 0.116 - 0.174: 34 0.174 - 0.233: 8 0.233 - 0.291: 4 Chirality restraints: 490 Sorted by residual: chirality pdb=" CB THR L 85 " pdb=" CA THR L 85 " pdb=" OG1 THR L 85 " pdb=" CG2 THR L 85 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL L 58 " pdb=" CA VAL L 58 " pdb=" CG1 VAL L 58 " pdb=" CG2 VAL L 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN E 354 " pdb=" N ASN E 354 " pdb=" C ASN E 354 " pdb=" CB ASN E 354 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 487 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO E 463 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.022 2.00e-02 2.50e+03 2.12e-02 9.01e+00 pdb=" CG TYR E 453 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO L 59 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.041 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 922 2.82 - 3.34: 2655 3.34 - 3.86: 5232 3.86 - 4.38: 5684 4.38 - 4.90: 10127 Nonbonded interactions: 24620 Sorted by model distance: nonbonded pdb=" O SER L 60 " pdb=" OG SER L 60 " model vdw 2.297 3.040 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.349 3.040 nonbonded pdb=" NH2 ARG H 67 " pdb=" OD2 ASP H 90 " model vdw 2.364 3.120 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.396 3.040 nonbonded pdb=" OG1 THR L 85 " pdb=" O GLY L 101 " model vdw 2.398 3.040 ... (remaining 24615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.640 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 3404 Z= 0.390 Angle : 1.201 11.712 4620 Z= 0.644 Chirality : 0.069 0.291 490 Planarity : 0.011 0.083 601 Dihedral : 14.445 89.737 1221 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.36), residues: 419 helix: -4.41 (0.43), residues: 30 sheet: -0.69 (0.47), residues: 125 loop : -2.41 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP H 117 HIS 0.002 0.001 HIS H 106 PHE 0.035 0.004 PHE E 377 TYR 0.050 0.003 TYR E 453 ARG 0.023 0.002 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.8113 (pttt) cc_final: 0.7753 (tptm) REVERT: L 27 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7296 (tm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1853 time to fit residues: 19.4805 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 0.0870 chunk 32 optimal weight: 0.0030 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.1666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.181865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.156161 restraints weight = 4298.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.156609 restraints weight = 4206.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158165 restraints weight = 3762.115| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3404 Z= 0.180 Angle : 0.636 7.065 4620 Z= 0.329 Chirality : 0.045 0.171 490 Planarity : 0.006 0.062 601 Dihedral : 5.643 32.109 470 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.67 % Allowed : 13.33 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.37), residues: 419 helix: -3.64 (0.71), residues: 30 sheet: -0.44 (0.48), residues: 119 loop : -2.33 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.003 0.001 HIS E 519 PHE 0.022 0.001 PHE E 456 TYR 0.013 0.001 TYR E 501 ARG 0.005 0.001 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.1830 time to fit residues: 18.2002 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139040 restraints weight = 4248.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139970 restraints weight = 3897.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141555 restraints weight = 3628.446| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3404 Z= 0.320 Angle : 0.706 8.438 4620 Z= 0.367 Chirality : 0.048 0.226 490 Planarity : 0.006 0.053 601 Dihedral : 5.979 35.506 470 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.50 % Allowed : 19.17 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.37), residues: 419 helix: -2.53 (1.05), residues: 24 sheet: -0.62 (0.48), residues: 117 loop : -2.12 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.026 0.003 PHE H 64 TYR 0.023 0.002 TYR L 49 ARG 0.009 0.001 ARG L 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 465 GLU cc_start: 0.7971 (pm20) cc_final: 0.7737 (pt0) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.2074 time to fit residues: 21.7379 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143038 restraints weight = 4304.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143407 restraints weight = 4036.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144834 restraints weight = 3674.979| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3404 Z= 0.218 Angle : 0.631 7.289 4620 Z= 0.324 Chirality : 0.045 0.189 490 Planarity : 0.005 0.052 601 Dihedral : 5.474 33.395 470 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.50 % Allowed : 21.67 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.38), residues: 419 helix: -2.01 (1.13), residues: 24 sheet: -0.55 (0.47), residues: 119 loop : -1.95 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.022 0.002 PHE E 456 TYR 0.015 0.001 TYR L 94 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 462 LYS cc_start: 0.8628 (mppt) cc_final: 0.8376 (mppt) REVERT: H 19 LYS cc_start: 0.7434 (tppp) cc_final: 0.7227 (tptt) REVERT: H 110 TYR cc_start: 0.7627 (t80) cc_final: 0.7364 (t80) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.2054 time to fit residues: 19.6027 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137424 restraints weight = 4255.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138535 restraints weight = 3858.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139689 restraints weight = 3493.353| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3404 Z= 0.290 Angle : 0.668 8.405 4620 Z= 0.347 Chirality : 0.047 0.219 490 Planarity : 0.005 0.050 601 Dihedral : 5.699 34.370 470 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.44 % Allowed : 20.56 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.37), residues: 419 helix: -2.75 (1.09), residues: 18 sheet: -0.68 (0.47), residues: 119 loop : -1.99 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.022 0.002 PHE H 64 TYR 0.018 0.002 TYR L 49 ARG 0.005 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 400 PHE cc_start: 0.8900 (m-80) cc_final: 0.8585 (m-80) REVERT: H 19 LYS cc_start: 0.7480 (tppp) cc_final: 0.7199 (tptt) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 0.2097 time to fit residues: 21.7933 Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 0.0020 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 overall best weight: 0.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN E 477 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144525 restraints weight = 4321.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144998 restraints weight = 3630.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147208 restraints weight = 3382.295| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3404 Z= 0.176 Angle : 0.614 7.792 4620 Z= 0.314 Chirality : 0.045 0.168 490 Planarity : 0.005 0.055 601 Dihedral : 5.227 31.325 470 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.61 % Allowed : 23.06 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.39), residues: 419 helix: -2.10 (1.06), residues: 24 sheet: -0.41 (0.49), residues: 119 loop : -1.81 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.028 0.001 PHE E 456 TYR 0.009 0.001 TYR E 423 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 LYS cc_start: 0.7513 (tppp) cc_final: 0.7254 (tptt) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.2070 time to fit residues: 20.3275 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 26 optimal weight: 0.0570 chunk 21 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN E 477 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142672 restraints weight = 4227.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142679 restraints weight = 3708.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144242 restraints weight = 3382.913| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3404 Z= 0.193 Angle : 0.615 8.139 4620 Z= 0.317 Chirality : 0.045 0.172 490 Planarity : 0.005 0.055 601 Dihedral : 5.103 29.845 470 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.61 % Allowed : 23.33 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.39), residues: 419 helix: -2.34 (1.15), residues: 18 sheet: -0.39 (0.49), residues: 118 loop : -1.73 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.029 0.002 PHE E 456 TYR 0.010 0.001 TYR L 49 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 LYS cc_start: 0.7500 (tppp) cc_final: 0.7240 (tptt) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.1993 time to fit residues: 19.9477 Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.2980 chunk 33 optimal weight: 0.0770 chunk 2 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139672 restraints weight = 4210.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139460 restraints weight = 4129.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140860 restraints weight = 3913.712| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3404 Z= 0.252 Angle : 0.654 8.074 4620 Z= 0.338 Chirality : 0.046 0.202 490 Planarity : 0.005 0.052 601 Dihedral : 5.307 31.789 470 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.89 % Allowed : 22.78 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.39), residues: 419 helix: -2.34 (1.16), residues: 18 sheet: -0.46 (0.49), residues: 119 loop : -1.77 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.029 0.002 PHE E 456 TYR 0.014 0.001 TYR L 49 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 400 PHE cc_start: 0.8757 (m-80) cc_final: 0.8542 (m-80) REVERT: E 467 ASP cc_start: 0.7634 (p0) cc_final: 0.7393 (p0) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.1930 time to fit residues: 18.6853 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 5 optimal weight: 0.0000 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140487 restraints weight = 4242.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141327 restraints weight = 3580.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142234 restraints weight = 2985.051| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3404 Z= 0.221 Angle : 0.656 8.505 4620 Z= 0.338 Chirality : 0.046 0.188 490 Planarity : 0.005 0.053 601 Dihedral : 5.250 30.854 470 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.61 % Allowed : 23.61 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.39), residues: 419 helix: -2.25 (1.19), residues: 18 sheet: -0.42 (0.49), residues: 119 loop : -1.73 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 36 HIS 0.000 0.000 HIS H 106 PHE 0.029 0.002 PHE E 456 TYR 0.011 0.001 TYR L 49 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: E 400 PHE cc_start: 0.8773 (m-80) cc_final: 0.8505 (m-80) REVERT: E 467 ASP cc_start: 0.7669 (p0) cc_final: 0.7436 (p0) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.2121 time to fit residues: 20.0208 Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.164470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137496 restraints weight = 4312.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136894 restraints weight = 3839.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138254 restraints weight = 3639.582| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3404 Z= 0.292 Angle : 0.692 8.467 4620 Z= 0.361 Chirality : 0.047 0.220 490 Planarity : 0.006 0.053 601 Dihedral : 5.544 32.678 470 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.78 % Allowed : 25.00 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.39), residues: 419 helix: -2.35 (1.17), residues: 18 sheet: -0.53 (0.49), residues: 118 loop : -1.84 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.028 0.002 PHE E 456 TYR 0.015 0.002 TYR L 49 ARG 0.008 0.001 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 400 PHE cc_start: 0.8876 (m-80) cc_final: 0.8602 (m-80) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.1967 time to fit residues: 18.4986 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.157518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132026 restraints weight = 4281.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133005 restraints weight = 3708.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134762 restraints weight = 3420.928| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3404 Z= 0.311 Angle : 0.714 8.750 4620 Z= 0.374 Chirality : 0.048 0.232 490 Planarity : 0.006 0.053 601 Dihedral : 5.721 33.959 470 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.50 % Allowed : 26.11 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.38), residues: 419 helix: -2.40 (1.15), residues: 18 sheet: -0.66 (0.49), residues: 118 loop : -1.91 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.027 0.002 PHE E 456 TYR 0.016 0.002 TYR L 49 ARG 0.008 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.78 seconds wall clock time: 29 minutes 38.52 seconds (1778.52 seconds total)