Starting phenix.real_space_refine on Wed Mar 5 18:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtj_32788/03_2025/7wtj_32788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtj_32788/03_2025/7wtj_32788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtj_32788/03_2025/7wtj_32788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtj_32788/03_2025/7wtj_32788.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtj_32788/03_2025/7wtj_32788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtj_32788/03_2025/7wtj_32788.cif" } resolution = 4.2 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= 0.003 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 14 5.16 5 C 2073 2.51 5 N 554 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3261 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Time building chain proxies: 3.55, per 1000 atoms: 1.09 Number of scatterers: 3261 At special positions: 0 Unit cell: (79.18, 82.39, 84.53, 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 14 16.00 O 620 8.00 N 554 7.00 C 2073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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: 0.82 Conformation dependent library (CDL) restraints added in 441.3 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 6.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.514A pdb=" N ASN E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.534A pdb=" N ALA E 352 " --> pdb=" O SER E 349 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.837A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.940A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.635A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 60 removed outlier: 3.718A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 117 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.797A pdb=" N SER L 64 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.617A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA L 90 " --> pdb=" O TYR L 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 398 through 403 removed outlier: 3.600A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 60 hydrogen bonds defined for protein. 138 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: 0.67 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 524 1.30 - 1.43: 986 1.43 - 1.56: 1826 1.56 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3352 Sorted by residual: bond pdb=" CA SER E 443 " pdb=" CB SER E 443 " ideal model delta sigma weight residual 1.532 1.378 0.154 1.68e-02 3.54e+03 8.41e+01 bond pdb=" CA SER E 438 " pdb=" CB SER E 438 " ideal model delta sigma weight residual 1.524 1.396 0.128 1.62e-02 3.81e+03 6.22e+01 bond pdb=" CA SER E 438 " pdb=" C SER E 438 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.18e-02 7.18e+03 3.07e+01 bond pdb=" C SER E 438 " pdb=" O SER E 438 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.22e-02 6.72e+03 1.88e+01 bond pdb=" C SER E 443 " pdb=" O SER E 443 " ideal model delta sigma weight residual 1.233 1.185 0.049 1.17e-02 7.31e+03 1.72e+01 ... (remaining 3347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4419 2.13 - 4.26: 113 4.26 - 6.39: 29 6.39 - 8.52: 5 8.52 - 10.65: 2 Bond angle restraints: 4568 Sorted by residual: angle pdb=" C ASP E 442 " pdb=" CA ASP E 442 " pdb=" CB ASP E 442 " ideal model delta sigma weight residual 111.88 101.23 10.65 1.41e+00 5.03e-01 5.71e+01 angle pdb=" C SER E 438 " pdb=" CA SER E 438 " pdb=" CB SER E 438 " ideal model delta sigma weight residual 111.82 102.80 9.02 1.38e+00 5.25e-01 4.27e+01 angle pdb=" O TRP E 436 " pdb=" C TRP E 436 " pdb=" N ASN E 437 " ideal model delta sigma weight residual 123.42 117.37 6.05 1.07e+00 8.73e-01 3.20e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA SER E 443 " pdb=" C SER E 443 " pdb=" O SER E 443 " ideal model delta sigma weight residual 121.38 116.07 5.31 1.06e+00 8.90e-01 2.51e+01 ... (remaining 4563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1752 17.35 - 34.71: 163 34.71 - 52.06: 32 52.06 - 69.41: 4 69.41 - 86.76: 5 Dihedral angle restraints: 1956 sinusoidal: 740 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 7.19 85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 150.75 -57.75 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA CYS E 391 " pdb=" C CYS E 391 " pdb=" N PHE E 392 " pdb=" CA PHE E 392 " ideal model delta harmonic sigma weight residual -180.00 -149.70 -30.30 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 1953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 390 0.057 - 0.113: 79 0.113 - 0.170: 10 0.170 - 0.227: 4 0.227 - 0.283: 2 Chirality restraints: 485 Sorted by residual: chirality pdb=" CA ASP H 55 " pdb=" N ASP H 55 " pdb=" C ASP H 55 " pdb=" CB ASP H 55 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN E 439 " pdb=" N ASN E 439 " pdb=" C ASN E 439 " pdb=" CB ASN E 439 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LYS E 440 " pdb=" N LYS E 440 " pdb=" C LYS E 440 " pdb=" CB LYS E 440 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 482 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 497 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C PHE E 497 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE E 497 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG E 498 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 54 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C GLY H 54 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY H 54 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP H 55 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 441 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C LEU E 441 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU E 441 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP E 442 " 0.015 2.00e-02 2.50e+03 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 649 2.77 - 3.31: 2916 3.31 - 3.84: 4813 3.84 - 4.37: 5398 4.37 - 4.90: 9724 Nonbonded interactions: 23500 Sorted by model distance: nonbonded pdb=" OG1 THR L 5 " pdb=" OG SER L 23 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG L 62 " pdb=" O SER L 77 " model vdw 2.292 3.120 nonbonded pdb=" O VAL E 367 " pdb=" ND2 ASN E 370 " model vdw 2.350 3.120 nonbonded pdb=" O ASP E 442 " pdb=" CB ASP E 442 " model vdw 2.369 2.752 nonbonded pdb=" O GLY L 78 " pdb=" NE ARG L 80 " model vdw 2.375 3.120 ... (remaining 23495 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 0.154 3352 Z= 0.395 Angle : 0.849 10.652 4568 Z= 0.520 Chirality : 0.052 0.283 485 Planarity : 0.006 0.047 593 Dihedral : 13.858 86.764 1170 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.58 % Allowed : 0.29 % Favored : 99.14 % Cbeta Deviations : 0.78 % 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 (0.40), residues: 418 helix: -3.24 (1.01), residues: 13 sheet: -0.37 (0.53), residues: 104 loop : -1.93 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE E 377 TYR 0.009 0.001 TYR E 495 ARG 0.002 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.349 Fit side-chains REVERT: H 82 GLU cc_start: 0.7106 (mp0) cc_final: 0.6621 (mp0) REVERT: E 441 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8301 (mt) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.1461 time to fit residues: 15.5436 Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN L 39 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097761 restraints weight = 6577.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098983 restraints weight = 4963.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099713 restraints weight = 4083.169| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 3352 Z= 0.491 Angle : 0.799 9.917 4568 Z= 0.420 Chirality : 0.051 0.166 485 Planarity : 0.006 0.049 593 Dihedral : 5.948 32.024 469 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.07 % Favored : 84.69 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.07 % 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: -2.81 (0.39), residues: 418 helix: -3.26 (0.83), residues: 25 sheet: -0.55 (0.54), residues: 105 loop : -2.42 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 101 HIS 0.005 0.002 HIS H 35 PHE 0.041 0.003 PHE H 64 TYR 0.013 0.002 TYR E 380 ARG 0.003 0.001 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.346 Fit side-chains REVERT: H 55 ASP cc_start: 0.8792 (p0) cc_final: 0.8235 (p0) REVERT: E 389 ASP cc_start: 0.6887 (p0) cc_final: 0.6675 (p0) REVERT: E 462 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8785 (mttm) outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.1178 time to fit residues: 12.3720 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN ** E 439 ASN ** 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 = 0.3443 r_free = 0.3443 target = 0.122470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101880 restraints weight = 6365.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102660 restraints weight = 5057.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103688 restraints weight = 4225.426| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3352 Z= 0.277 Angle : 0.662 7.736 4568 Z= 0.341 Chirality : 0.047 0.169 485 Planarity : 0.005 0.047 593 Dihedral : 5.464 29.222 469 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.39), residues: 418 helix: -2.75 (1.09), residues: 19 sheet: -0.25 (0.51), residues: 105 loop : -2.12 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 92 HIS 0.002 0.001 HIS E 519 PHE 0.020 0.002 PHE H 64 TYR 0.018 0.001 TYR L 50 ARG 0.002 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.347 Fit side-chains REVERT: H 55 ASP cc_start: 0.8670 (p0) cc_final: 0.8068 (p0) REVERT: L 76 ILE cc_start: 0.8158 (mp) cc_final: 0.7894 (mm) REVERT: E 389 ASP cc_start: 0.6975 (p0) cc_final: 0.6673 (p0) REVERT: E 424 LYS cc_start: 0.7845 (ptmt) cc_final: 0.7599 (ptmt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1345 time to fit residues: 13.6643 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.121881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101176 restraints weight = 6476.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102215 restraints weight = 5103.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103097 restraints weight = 4151.113| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3352 Z= 0.266 Angle : 0.660 7.945 4568 Z= 0.340 Chirality : 0.047 0.164 485 Planarity : 0.005 0.049 593 Dihedral : 5.442 30.094 469 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.96 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -2.24 (0.39), residues: 418 helix: -2.92 (1.02), residues: 19 sheet: -0.01 (0.52), residues: 102 loop : -2.09 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 92 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE H 64 TYR 0.016 0.001 TYR L 50 ARG 0.005 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.299 Fit side-chains REVERT: H 55 ASP cc_start: 0.8766 (p0) cc_final: 0.8244 (p0) REVERT: L 76 ILE cc_start: 0.8163 (mp) cc_final: 0.7874 (mm) REVERT: E 389 ASP cc_start: 0.6960 (p0) cc_final: 0.6614 (p0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1182 time to fit residues: 12.0735 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 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 = 0.3365 r_free = 0.3365 target = 0.117225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096409 restraints weight = 6587.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098042 restraints weight = 4233.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098806 restraints weight = 3518.328| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 3352 Z= 0.497 Angle : 0.805 8.464 4568 Z= 0.420 Chirality : 0.052 0.175 485 Planarity : 0.006 0.048 593 Dihedral : 6.165 28.556 469 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.03 % Favored : 83.73 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.38), residues: 418 helix: -3.74 (0.74), residues: 25 sheet: -0.29 (0.52), residues: 102 loop : -2.36 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP L 101 HIS 0.005 0.002 HIS H 35 PHE 0.029 0.003 PHE E 374 TYR 0.027 0.002 TYR L 37 ARG 0.006 0.001 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7188 (p0) cc_final: 0.6929 (p0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1381 time to fit residues: 13.9785 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102178 restraints weight = 6542.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104476 restraints weight = 4298.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105563 restraints weight = 3503.264| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3352 Z= 0.184 Angle : 0.654 8.027 4568 Z= 0.334 Chirality : 0.046 0.168 485 Planarity : 0.004 0.048 593 Dihedral : 5.438 32.581 469 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -2.24 (0.39), residues: 418 helix: -2.93 (1.01), residues: 19 sheet: -0.15 (0.51), residues: 102 loop : -2.03 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 111 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE H 64 TYR 0.012 0.001 TYR L 50 ARG 0.003 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.348 Fit side-chains REVERT: H 70 LEU cc_start: 0.9201 (tp) cc_final: 0.8913 (tt) REVERT: E 389 ASP cc_start: 0.6878 (p0) cc_final: 0.6553 (p0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1239 time to fit residues: 12.3089 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.123882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103292 restraints weight = 6340.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103670 restraints weight = 4850.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104810 restraints weight = 3922.653| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3352 Z= 0.181 Angle : 0.672 10.422 4568 Z= 0.340 Chirality : 0.047 0.165 485 Planarity : 0.004 0.048 593 Dihedral : 5.218 30.103 469 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.57 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -2.20 (0.39), residues: 418 helix: -3.08 (0.98), residues: 19 sheet: -0.13 (0.49), residues: 103 loop : -1.99 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 111 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE H 64 TYR 0.026 0.001 TYR L 50 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.401 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1368 time to fit residues: 13.4121 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102228 restraints weight = 6316.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102849 restraints weight = 4897.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103906 restraints weight = 4123.937| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3352 Z= 0.264 Angle : 0.704 10.116 4568 Z= 0.360 Chirality : 0.047 0.172 485 Planarity : 0.005 0.048 593 Dihedral : 5.497 32.146 469 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.48 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.28 (0.39), residues: 418 helix: -2.67 (1.13), residues: 19 sheet: -0.20 (0.50), residues: 103 loop : -2.08 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 101 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.002 PHE H 64 TYR 0.022 0.001 TYR L 50 ARG 0.003 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.321 Fit side-chains REVERT: E 424 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7918 (ptmt) REVERT: E 493 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7645 (ttm170) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1425 time to fit residues: 13.8604 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.124994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104463 restraints weight = 6286.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105254 restraints weight = 4779.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106321 restraints weight = 3805.484| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3352 Z= 0.183 Angle : 0.646 8.148 4568 Z= 0.324 Chirality : 0.046 0.160 485 Planarity : 0.004 0.048 593 Dihedral : 5.232 32.820 469 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.09 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.22 (0.39), residues: 418 helix: -2.91 (1.21), residues: 13 sheet: -0.25 (0.48), residues: 105 loop : -2.02 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 92 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.001 PHE H 64 TYR 0.032 0.001 TYR L 50 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.361 Fit side-chains REVERT: L 50 TYR cc_start: 0.6744 (m-80) cc_final: 0.6461 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1379 time to fit residues: 13.4297 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.0030 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.127006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107004 restraints weight = 6193.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107851 restraints weight = 4603.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108942 restraints weight = 3765.762| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3352 Z= 0.181 Angle : 0.648 8.783 4568 Z= 0.323 Chirality : 0.046 0.157 485 Planarity : 0.005 0.049 593 Dihedral : 5.121 31.986 469 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.17 (0.39), residues: 418 helix: -2.94 (1.19), residues: 13 sheet: -0.24 (0.48), residues: 105 loop : -1.97 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE H 64 TYR 0.027 0.001 TYR L 50 ARG 0.002 0.000 ARG E 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.360 Fit side-chains REVERT: L 50 TYR cc_start: 0.6779 (m-80) cc_final: 0.6412 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1243 time to fit residues: 12.0192 Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.123894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103628 restraints weight = 6402.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104129 restraints weight = 5071.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105202 restraints weight = 4092.518| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3352 Z= 0.252 Angle : 0.675 8.680 4568 Z= 0.340 Chirality : 0.047 0.168 485 Planarity : 0.005 0.048 593 Dihedral : 5.387 34.352 469 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.00 % Favored : 88.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.29 (0.39), residues: 418 helix: -2.80 (1.05), residues: 19 sheet: -0.31 (0.49), residues: 103 loop : -2.03 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 101 HIS 0.006 0.002 HIS H 35 PHE 0.021 0.002 PHE H 64 TYR 0.026 0.001 TYR L 50 ARG 0.002 0.000 ARG E 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.03 seconds wall clock time: 26 minutes 7.42 seconds (1567.42 seconds total)