Starting phenix.real_space_refine on Mon Feb 10 23:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtj_32788/02_2025/7wtj_32788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtj_32788/02_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_32788/02_2025/7wtj_32788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtj_32788/02_2025/7wtj_32788.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtj_32788/02_2025/7wtj_32788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtj_32788/02_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-5592/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: 3.08, per 1000 atoms: 0.94 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: 0.76 Conformation dependent library (CDL) restraints added in 401.4 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: 0.30 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: 0.66 Time building geometry restraints manager: 0.91 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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 : 0.397 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: 0.1509 time to fit residues: 16.0230 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 : 0.344 ------------------------------------------------------------------------------- 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 = 0.097760 restraints weight = 6577.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098980 restraints weight = 4963.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099716 restraints weight = 4083.994| |-----------------------------------------------------------------------------| 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 : 0.339 Fit side-chains REVERT: H 55 ASP cc_start: 0.8792 (p0) cc_final: 0.8235 (p0) REVERT: E 389 ASP cc_start: 0.6886 (p0) cc_final: 0.6675 (p0) REVERT: E 462 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8784 (mttm) outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.1247 time to fit residues: 12.9846 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 : 0.359 ------------------------------------------------------------------------------- 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: 0.0770 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101877 restraints weight = 6368.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102657 restraints weight = 5033.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103687 restraints weight = 4195.686| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2070 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= 0.268 Angle : 0.658 7.658 4568 Z= 0.339 Chirality : 0.047 0.168 485 Planarity : 0.005 0.047 593 Dihedral : 5.443 29.209 469 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: -2.32 (0.39), residues: 418 helix: -2.73 (1.10), residues: 19 sheet: -0.24 (0.51), residues: 105 loop : -2.11 (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 0.022 0.002 PHE H 64 TYR 0.019 0.001 TYR L 50 ARG 0.002 0.000 ARG E 466 *********************** 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 82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.385 Fit side-chains REVERT: H 55 ASP cc_start: 0.8687 (p0) cc_final: 0.8097 (p0) REVERT: L 76 ILE cc_start: 0.8153 (mp) cc_final: 0.7887 (mm) REVERT: E 389 ASP cc_start: 0.6950 (p0) cc_final: 0.6644 (p0) REVERT: E 424 LYS cc_start: 0.7840 (ptmt) cc_final: 0.7598 (ptmt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1375 time to fit residues: 14.0560 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 : 0.365 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.122013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101331 restraints weight = 6456.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102100 restraints weight = 5156.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103045 restraints weight = 4163.329| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3352 Z= 0.268 Angle : 0.663 7.952 4568 Z= 0.341 Chirality : 0.047 0.164 485 Planarity : 0.005 0.049 593 Dihedral : 5.448 30.439 469 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.24 % Favored : 88.52 % 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: -2.22 (0.39), residues: 418 helix: -2.90 (1.02), residues: 19 sheet: -0.02 (0.51), residues: 102 loop : -2.06 (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 0.010 0.002 PHE E 374 TYR 0.016 0.001 TYR L 50 ARG 0.004 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 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.343 Fit side-chains REVERT: H 55 ASP cc_start: 0.8759 (p0) cc_final: 0.8246 (p0) REVERT: L 76 ILE cc_start: 0.8161 (mp) cc_final: 0.7871 (mm) REVERT: E 389 ASP cc_start: 0.6977 (p0) cc_final: 0.6609 (p0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1366 time to fit residues: 13.7978 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 : 0.365 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.117248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096418 restraints weight = 6592.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098111 restraints weight = 4279.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098868 restraints weight = 3482.506| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2612 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= 0.476 Angle : 0.805 8.547 4568 Z= 0.420 Chirality : 0.052 0.169 485 Planarity : 0.006 0.048 593 Dihedral : 6.112 28.070 469 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.03 % Favored : 83.73 % Rotamer: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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: -2.58 (0.38), residues: 418 helix: -3.10 (0.96), residues: 19 sheet: -0.25 (0.51), residues: 102 loop : -2.33 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 101 HIS 0.005 0.002 HIS H 35 PHE 0.026 0.003 PHE E 374 TYR 0.028 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 : 0.394 Fit side-chains revert: symmetry clash REVERT: H 118 THR cc_start: 0.9235 (p) cc_final: 0.9030 (p) REVERT: E 389 ASP cc_start: 0.7177 (p0) cc_final: 0.6917 (p0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1402 time to fit residues: 14.1678 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 : 0.412 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 29 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.123182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102514 restraints weight = 6541.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103962 restraints weight = 4542.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105001 restraints weight = 3844.598| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3352 Z= 0.186 Angle : 0.648 8.053 4568 Z= 0.332 Chirality : 0.046 0.167 485 Planarity : 0.005 0.048 593 Dihedral : 5.382 31.833 469 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -2.30 (0.39), residues: 418 helix: -2.94 (1.01), residues: 19 sheet: -0.18 (0.50), residues: 103 loop : -2.09 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 111 HIS 0.004 0.001 HIS H 35 PHE 0.007 0.001 PHE H 108 TYR 0.013 0.001 TYR L 37 ARG 0.002 0.000 ARG H 38 *********************** 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 : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1221 time to fit residues: 12.1444 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 : 0.310 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.122559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101792 restraints weight = 6358.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102850 restraints weight = 4481.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103758 restraints weight = 3514.194| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3352 Z= 0.226 Angle : 0.699 11.372 4568 Z= 0.355 Chirality : 0.047 0.187 485 Planarity : 0.005 0.048 593 Dihedral : 5.396 29.877 469 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.53 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -2.33 (0.39), residues: 418 helix: -3.09 (0.96), residues: 19 sheet: -0.17 (0.49), residues: 103 loop : -2.11 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 92 HIS 0.006 0.002 HIS H 35 PHE 0.008 0.001 PHE H 108 TYR 0.025 0.001 TYR L 50 ARG 0.003 0.000 ARG E 509 *********************** 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 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1486 time to fit residues: 14.7678 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 : 0.380 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.123276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102636 restraints weight = 6310.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103344 restraints weight = 4525.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104355 restraints weight = 3654.559| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3352 Z= 0.235 Angle : 0.687 10.155 4568 Z= 0.350 Chirality : 0.047 0.177 485 Planarity : 0.005 0.048 593 Dihedral : 5.462 31.843 469 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.29 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -2.32 (0.39), residues: 418 helix: -2.66 (1.13), residues: 19 sheet: -0.22 (0.49), residues: 103 loop : -2.11 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 92 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.002 PHE E 374 TYR 0.023 0.001 TYR L 50 ARG 0.003 0.000 ARG E 493 *********************** 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 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1404 time to fit residues: 13.9532 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.0470 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.0470 chunk 35 optimal weight: 0.0270 overall best weight: 0.1492 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.128412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106011 restraints weight = 6231.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108396 restraints weight = 4341.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110026 restraints weight = 3307.656| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 3352 Z= 0.162 Angle : 0.630 8.131 4568 Z= 0.314 Chirality : 0.045 0.158 485 Planarity : 0.004 0.048 593 Dihedral : 5.021 29.719 469 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % 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 : 0.00 % 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: -2.09 (0.39), residues: 418 helix: -3.04 (1.15), residues: 13 sheet: -0.14 (0.49), residues: 103 loop : -1.90 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 111 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE H 64 TYR 0.033 0.001 TYR L 50 ARG 0.003 0.000 ARG L 55 *********************** 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 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.381 Fit side-chains REVERT: H 50 ILE cc_start: 0.9015 (tp) cc_final: 0.8799 (tp) REVERT: L 50 TYR cc_start: 0.6584 (m-80) cc_final: 0.6316 (m-80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1396 time to fit residues: 13.7312 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 : 0.375 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.124729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104231 restraints weight = 6285.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105076 restraints weight = 4556.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106147 restraints weight = 3637.306| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 3352 Z= 0.233 Angle : 0.658 8.466 4568 Z= 0.333 Chirality : 0.046 0.163 485 Planarity : 0.005 0.049 593 Dihedral : 5.283 33.386 469 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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: -2.23 (0.39), residues: 418 helix: -2.76 (1.06), residues: 19 sheet: -0.21 (0.49), residues: 103 loop : -2.00 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 36 HIS 0.006 0.002 HIS H 35 PHE 0.018 0.002 PHE H 64 TYR 0.024 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 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.342 Fit side-chains REVERT: L 50 TYR cc_start: 0.6859 (m-80) cc_final: 0.6511 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1264 time to fit residues: 11.8959 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 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 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.126354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105769 restraints weight = 6352.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107038 restraints weight = 4662.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107951 restraints weight = 3513.410| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3352 Z= 0.188 Angle : 0.641 8.395 4568 Z= 0.321 Chirality : 0.045 0.162 485 Planarity : 0.005 0.049 593 Dihedral : 5.173 33.111 469 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -2.18 (0.39), residues: 418 helix: -2.78 (1.06), residues: 19 sheet: -0.26 (0.49), residues: 103 loop : -1.94 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.001 PHE H 64 TYR 0.025 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: 1432.06 seconds wall clock time: 26 minutes 20.21 seconds (1580.21 seconds total)