Starting phenix.real_space_refine on Sun Mar 10 16:08:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtj_32788/03_2024/7wtj_32788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtj_32788/03_2024/7wtj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtj_32788/03_2024/7wtj_32788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtj_32788/03_2024/7wtj_32788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtj_32788/03_2024/7wtj_32788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtj_32788/03_2024/7wtj_32788.pdb" } 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 Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E ASP 427": "OD1" <-> "OD2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.07, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.16 Conformation dependent library (CDL) restraints added in 544.9 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: 0.29 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: 0.64 Time building geometry restraints manager: 1.28 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: 100.28 - 107.02: 130 107.02 - 113.76: 1721 113.76 - 120.50: 1240 120.50 - 127.24: 1437 127.24 - 133.98: 40 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 2.440 nonbonded pdb=" NH1 ARG L 62 " pdb=" O SER L 77 " model vdw 2.292 2.520 nonbonded pdb=" O VAL E 367 " pdb=" ND2 ASN E 370 " model vdw 2.350 2.520 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 2.520 ... (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 ========== 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 9.970 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.365 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: 0.1563 time to fit residues: 16.6041 Evaluate side-chains 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.0770 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0010 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.7146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN E 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 3352 Z= 0.209 Angle : 0.605 8.056 4568 Z= 0.310 Chirality : 0.044 0.153 485 Planarity : 0.004 0.046 593 Dihedral : 4.836 25.532 469 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -2.25 (0.40), residues: 418 helix: -3.38 (0.93), residues: 19 sheet: -0.05 (0.55), residues: 99 loop : -2.03 (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 0.025 0.001 PHE H 64 TYR 0.007 0.001 TYR L 50 ARG 0.002 0.000 ARG E 454 *********************** 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 84 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.375 Fit side-chains REVERT: H 55 ASP cc_start: 0.8626 (p0) cc_final: 0.7897 (p0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1139 time to fit residues: 12.3661 Evaluate side-chains 74 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 36 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.0020 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 overall best weight: 0.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 3352 Z= 0.146 Angle : 0.559 7.751 4568 Z= 0.277 Chirality : 0.044 0.161 485 Planarity : 0.004 0.048 593 Dihedral : 4.487 23.260 469 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % 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 : 0.00 % 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: -2.06 (0.40), residues: 418 helix: -3.32 (0.96), residues: 19 sheet: 0.10 (0.50), residues: 107 loop : -1.95 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 111 HIS 0.001 0.000 HIS E 519 PHE 0.006 0.001 PHE H 64 TYR 0.016 0.001 TYR L 50 ARG 0.001 0.000 ARG H 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 85 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.406 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1346 time to fit residues: 14.3719 Evaluate side-chains 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3352 Z= 0.257 Angle : 0.620 7.943 4568 Z= 0.315 Chirality : 0.045 0.153 485 Planarity : 0.005 0.048 593 Dihedral : 4.874 27.252 469 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % 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 : 0.00 % 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: -2.08 (0.40), residues: 418 helix: -3.26 (0.99), residues: 19 sheet: 0.11 (0.50), residues: 107 loop : -1.98 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE L 103 TYR 0.014 0.001 TYR L 37 ARG 0.003 0.000 ARG E 466 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.357 Fit side-chains REVERT: E 474 GLN cc_start: 0.7103 (tt0) cc_final: 0.6854 (tt0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1187 time to fit residues: 12.4402 Evaluate side-chains 71 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1844 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= 0.252 Angle : 0.633 8.138 4568 Z= 0.322 Chirality : 0.045 0.160 485 Planarity : 0.005 0.048 593 Dihedral : 5.043 29.452 469 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % 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: -2.14 (0.40), residues: 418 helix: -3.01 (0.94), residues: 25 sheet: -0.00 (0.49), residues: 107 loop : -1.97 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 107 HIS 0.005 0.002 HIS H 35 PHE 0.017 0.001 PHE H 64 TYR 0.012 0.001 TYR L 50 ARG 0.003 0.000 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 fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.530 Fit side-chains REVERT: E 389 ASP cc_start: 0.6454 (p0) cc_final: 0.6159 (p0) REVERT: E 474 GLN cc_start: 0.7127 (tt0) cc_final: 0.6890 (tt0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1263 time to fit residues: 13.1682 Evaluate side-chains 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3352 Z= 0.192 Angle : 0.602 8.164 4568 Z= 0.302 Chirality : 0.044 0.155 485 Planarity : 0.004 0.047 593 Dihedral : 4.913 25.449 469 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: -1.92 (0.40), residues: 418 helix: -2.92 (1.21), residues: 13 sheet: 0.03 (0.49), residues: 107 loop : -1.84 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE H 64 TYR 0.010 0.001 TYR L 37 ARG 0.002 0.000 ARG L 55 *********************** 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 fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.370 Fit side-chains REVERT: E 474 GLN cc_start: 0.7096 (tt0) cc_final: 0.6821 (tt0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1256 time to fit residues: 12.4871 Evaluate side-chains 68 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3352 Z= 0.171 Angle : 0.593 7.811 4568 Z= 0.297 Chirality : 0.044 0.152 485 Planarity : 0.004 0.047 593 Dihedral : 4.772 26.553 469 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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: -1.92 (0.40), residues: 418 helix: -2.79 (1.29), residues: 13 sheet: -0.02 (0.49), residues: 109 loop : -1.82 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 64 TYR 0.010 0.001 TYR L 37 ARG 0.001 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 79 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.748 Fit side-chains REVERT: E 389 ASP cc_start: 0.6160 (p0) cc_final: 0.5883 (p0) REVERT: E 474 GLN cc_start: 0.7029 (tt0) cc_final: 0.6817 (tt0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1474 time to fit residues: 15.1014 Evaluate side-chains 66 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2047 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= 0.183 Angle : 0.612 7.954 4568 Z= 0.304 Chirality : 0.045 0.168 485 Planarity : 0.004 0.048 593 Dihedral : 4.872 32.254 469 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % 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: -1.92 (0.40), residues: 418 helix: -2.61 (1.41), residues: 13 sheet: 0.06 (0.49), residues: 110 loop : -1.88 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 111 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE H 64 TYR 0.009 0.001 TYR L 37 ARG 0.001 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 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1258 time to fit residues: 12.1013 Evaluate side-chains 66 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3352 Z= 0.202 Angle : 0.631 9.987 4568 Z= 0.312 Chirality : 0.045 0.165 485 Planarity : 0.004 0.049 593 Dihedral : 4.903 32.830 469 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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: -1.96 (0.40), residues: 418 helix: -2.66 (1.38), residues: 13 sheet: -0.01 (0.49), residues: 110 loop : -1.89 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 101 HIS 0.006 0.002 HIS H 35 PHE 0.013 0.001 PHE H 64 TYR 0.005 0.001 TYR L 37 ARG 0.002 0.000 ARG E 509 *********************** 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 fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.374 Fit side-chains REVERT: H 50 ILE cc_start: 0.8959 (tp) cc_final: 0.8751 (tp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1261 time to fit residues: 12.4681 Evaluate side-chains 66 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 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 33 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0000 chunk 4 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 0.0370 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 3352 Z= 0.157 Angle : 0.603 8.889 4568 Z= 0.296 Chirality : 0.044 0.161 485 Planarity : 0.004 0.050 593 Dihedral : 4.742 31.044 469 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % 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: -1.77 (0.41), residues: 418 helix: -2.76 (1.32), residues: 13 sheet: 0.36 (0.50), residues: 103 loop : -1.81 (0.36), residues: 302 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 0.008 0.001 PHE E 490 TYR 0.010 0.001 TYR H 32 ARG 0.001 0.000 ARG H 38 ********************** 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 84 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1617 time to fit residues: 16.3851 Evaluate side-chains 65 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.125099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104584 restraints weight = 6411.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104887 restraints weight = 5307.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105861 restraints weight = 4302.417| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3352 Z= 0.270 Angle : 0.677 9.186 4568 Z= 0.342 Chirality : 0.046 0.168 485 Planarity : 0.005 0.049 593 Dihedral : 5.203 34.495 469 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % 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: -1.92 (0.40), residues: 418 helix: -2.71 (1.34), residues: 13 sheet: 0.23 (0.50), residues: 103 loop : -1.91 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.007 0.002 HIS H 35 PHE 0.017 0.002 PHE E 374 TYR 0.010 0.001 TYR L 37 ARG 0.005 0.001 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.41 seconds wall clock time: 24 minutes 6.49 seconds (1446.49 seconds total)