Starting phenix.real_space_refine on Thu Jul 18 22:08:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/07_2024/7uuy_26806.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/07_2024/7uuy_26806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/07_2024/7uuy_26806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/07_2024/7uuy_26806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/07_2024/7uuy_26806.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/07_2024/7uuy_26806.cif" } resolution = 3.3 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= 0.003 sd= 0.062 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 2512 2.51 5 N 601 2.21 5 O 668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3809 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3767 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain breaks: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 2.88, per 1000 atoms: 0.76 Number of scatterers: 3809 At special positions: 0 Unit cell: (66.216, 85.44, 85.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 668 8.00 N 601 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " 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: 1.59 Conformation dependent library (CDL) restraints added in 701.0 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 4.277A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 69 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 101 removed outlier: 4.034A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.624A pdb=" N LEU A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.710A pdb=" N GLU A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 161 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 164 through 180 Processing helix chain 'A' and resid 190 through 213 removed outlier: 4.173A pdb=" N VAL A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.559A pdb=" N LEU A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 removed outlier: 4.036A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.855A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 370 removed outlier: 3.643A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.145A pdb=" N ARG A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 removed outlier: 4.294A pdb=" N LYS A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.624A pdb=" N GLY A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 4.118A pdb=" N LEU A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.568A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.509A pdb=" N GLY A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.327A pdb=" N GLY A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.645A pdb=" N LEU A 553 " --> pdb=" O ARG A 550 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 792 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: 0.95 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 615 1.33 - 1.45: 1036 1.45 - 1.57: 2202 1.57 - 1.69: 2 1.69 - 1.82: 42 Bond restraints: 3897 Sorted by residual: bond pdb=" O14 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.527 1.654 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" O11 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.703 1.645 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.526 1.491 0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" O13 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 3PH A 701 " pdb=" O11 3PH A 701 " ideal model delta sigma weight residual 1.385 1.409 -0.024 2.00e-02 2.50e+03 1.47e+00 ... (remaining 3892 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 126 106.81 - 113.61: 2186 113.61 - 120.40: 1567 120.40 - 127.20: 1386 127.20 - 134.00: 48 Bond angle restraints: 5313 Sorted by residual: angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 112.29 108.82 3.47 9.40e-01 1.13e+00 1.36e+01 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O14 3PH A 701 " ideal model delta sigma weight residual 113.84 104.61 9.23 3.00e+00 1.11e-01 9.48e+00 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O13 3PH A 701 " ideal model delta sigma weight residual 115.12 123.51 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 118.57 -5.87 3.00e+00 1.11e-01 3.82e+00 angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 112.49 110.13 2.36 1.21e+00 6.83e-01 3.81e+00 ... (remaining 5308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2041 15.79 - 31.58: 162 31.58 - 47.37: 39 47.37 - 63.16: 10 63.16 - 78.96: 6 Dihedral angle restraints: 2258 sinusoidal: 838 harmonic: 1420 Sorted by residual: dihedral pdb=" CA LEU A 558 " pdb=" CB LEU A 558 " pdb=" CG LEU A 558 " pdb=" CD1 LEU A 558 " ideal model delta sinusoidal sigma weight residual 180.00 123.13 56.87 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN A 136 " pdb=" CA GLN A 136 " pdb=" CB GLN A 136 " pdb=" CG GLN A 136 " ideal model delta sinusoidal sigma weight residual -180.00 -123.34 -56.66 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N ASN A 97 " pdb=" CA ASN A 97 " pdb=" CB ASN A 97 " pdb=" CG ASN A 97 " ideal model delta sinusoidal sigma weight residual 60.00 116.64 -56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 489 0.039 - 0.078: 122 0.078 - 0.117: 24 0.117 - 0.156: 0 0.156 - 0.195: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" C2 3PH A 701 " pdb=" C1 3PH A 701 " pdb=" C3 3PH A 701 " pdb=" O21 3PH A 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CA PRO A 312 " pdb=" N PRO A 312 " pdb=" C PRO A 312 " pdb=" CB PRO A 312 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.20e-01 ... (remaining 633 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 195 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C VAL A 195 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 195 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 311 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 312 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C PHE A 247 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 42 2.63 - 3.20: 3759 3.20 - 3.77: 5984 3.77 - 4.33: 8119 4.33 - 4.90: 13789 Nonbonded interactions: 31693 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLN A 265 " model vdw 2.067 2.520 nonbonded pdb=" O HIS A 273 " pdb=" OG1 THR A 274 " model vdw 2.097 2.440 nonbonded pdb=" ND2 ASN A 441 " pdb=" O GLY A 546 " model vdw 2.211 2.520 nonbonded pdb=" OD1 ASP A 311 " pdb=" OH TYR A 324 " model vdw 2.228 2.440 nonbonded pdb=" O HIS A 226 " pdb=" OG SER A 227 " model vdw 2.332 2.440 ... (remaining 31688 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 individual isotropic 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: 0.970 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 3897 Z= 0.264 Angle : 0.580 9.235 5313 Z= 0.291 Chirality : 0.035 0.195 636 Planarity : 0.004 0.045 644 Dihedral : 13.503 78.955 1357 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.25 % Allowed : 10.83 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.41), residues: 495 helix: 1.24 (0.30), residues: 359 sheet: None (None), residues: 0 loop : -1.54 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 15 HIS 0.001 0.000 HIS A 273 PHE 0.010 0.001 PHE A 304 TYR 0.023 0.001 TYR A 17 ARG 0.006 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.6749 (mtm) cc_final: 0.6330 (mtp) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1425 time to fit residues: 10.8259 Evaluate side-chains 57 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3897 Z= 0.228 Angle : 0.569 7.922 5313 Z= 0.285 Chirality : 0.039 0.160 636 Planarity : 0.004 0.045 644 Dihedral : 7.980 86.575 579 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.02 % Allowed : 10.58 % Favored : 87.41 % 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: 1.32 (0.41), residues: 495 helix: 1.66 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.40 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 559 HIS 0.002 0.001 HIS A 273 PHE 0.013 0.002 PHE A 12 TYR 0.016 0.001 TYR A 17 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.475 Fit side-chains REVERT: A 198 MET cc_start: 0.6517 (mtm) cc_final: 0.6127 (mtm) REVERT: A 516 ASP cc_start: 0.7980 (t0) cc_final: 0.7727 (t0) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1329 time to fit residues: 10.6046 Evaluate side-chains 55 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3897 Z= 0.248 Angle : 0.557 6.689 5313 Z= 0.276 Chirality : 0.039 0.165 636 Planarity : 0.004 0.045 644 Dihedral : 7.882 88.652 579 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 13.35 % Favored : 84.38 % 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: 1.50 (0.40), residues: 495 helix: 1.80 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.32 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.001 0.001 HIS A 226 PHE 0.028 0.002 PHE A 12 TYR 0.014 0.001 TYR A 17 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.447 Fit side-chains REVERT: A 516 ASP cc_start: 0.7947 (t0) cc_final: 0.7621 (t0) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.1303 time to fit residues: 9.6778 Evaluate side-chains 54 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.0020 chunk 45 optimal weight: 0.0570 chunk 48 optimal weight: 0.4980 chunk 43 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3897 Z= 0.179 Angle : 0.523 7.247 5313 Z= 0.258 Chirality : 0.037 0.194 636 Planarity : 0.004 0.042 644 Dihedral : 7.712 88.111 579 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.76 % Allowed : 15.62 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.41), residues: 495 helix: 2.13 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.38 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.038 0.002 PHE A 12 TYR 0.014 0.001 TYR A 17 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.417 Fit side-chains REVERT: A 11 THR cc_start: 0.8238 (m) cc_final: 0.7924 (p) REVERT: A 516 ASP cc_start: 0.7865 (t0) cc_final: 0.7480 (t0) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.1335 time to fit residues: 10.8446 Evaluate side-chains 54 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 0.0040 chunk 12 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 28 optimal weight: 0.0980 overall best weight: 0.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 3897 Z= 0.166 Angle : 0.521 7.482 5313 Z= 0.257 Chirality : 0.037 0.190 636 Planarity : 0.004 0.040 644 Dihedral : 7.459 87.282 579 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.02 % Allowed : 16.88 % Favored : 81.11 % 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 (0.41), residues: 495 helix: 2.07 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.13 (0.62), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.001 0.000 HIS A 226 PHE 0.022 0.001 PHE A 12 TYR 0.012 0.001 TYR A 269 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.403 Fit side-chains REVERT: A 17 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: A 67 PHE cc_start: 0.7985 (t80) cc_final: 0.7714 (t80) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1128 time to fit residues: 9.2203 Evaluate side-chains 61 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3897 Z= 0.239 Angle : 0.544 8.243 5313 Z= 0.265 Chirality : 0.039 0.190 636 Planarity : 0.004 0.041 644 Dihedral : 7.525 85.991 579 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.02 % Allowed : 17.88 % Favored : 80.10 % 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: 1.84 (0.40), residues: 495 helix: 2.05 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.25 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 458 HIS 0.001 0.000 HIS A 226 PHE 0.017 0.002 PHE A 12 TYR 0.011 0.001 TYR A 118 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.440 Fit side-chains REVERT: A 17 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6515 (m-80) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.1219 time to fit residues: 8.5772 Evaluate side-chains 55 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.0170 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3897 Z= 0.159 Angle : 0.514 7.440 5313 Z= 0.252 Chirality : 0.037 0.183 636 Planarity : 0.004 0.040 644 Dihedral : 7.385 84.419 579 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 17.63 % Favored : 80.10 % 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: 2.05 (0.41), residues: 495 helix: 2.24 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.29 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.001 0.000 HIS A 226 PHE 0.014 0.001 PHE A 12 TYR 0.016 0.001 TYR A 269 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.423 Fit side-chains REVERT: A 12 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: A 17 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: A 292 ILE cc_start: 0.8009 (mm) cc_final: 0.7790 (mt) REVERT: A 324 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7976 (m-80) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.1161 time to fit residues: 9.0889 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.0040 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3897 Z= 0.199 Angle : 0.527 7.440 5313 Z= 0.257 Chirality : 0.038 0.179 636 Planarity : 0.004 0.040 644 Dihedral : 7.252 83.293 579 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.52 % Allowed : 17.88 % Favored : 79.60 % 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: 2.04 (0.41), residues: 495 helix: 2.23 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.27 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 458 HIS 0.000 0.000 HIS A 226 PHE 0.016 0.002 PHE A 12 TYR 0.014 0.001 TYR A 269 ARG 0.006 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.395 Fit side-chains REVERT: A 12 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: A 17 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: A 23 MET cc_start: 0.7644 (tpp) cc_final: 0.7104 (ttm) REVERT: A 292 ILE cc_start: 0.8081 (mm) cc_final: 0.7880 (mt) REVERT: A 324 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8005 (m-80) outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1310 time to fit residues: 9.7412 Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3897 Z= 0.212 Angle : 0.577 15.206 5313 Z= 0.274 Chirality : 0.038 0.172 636 Planarity : 0.004 0.040 644 Dihedral : 7.166 82.329 579 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.77 % Allowed : 17.88 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.41), residues: 495 helix: 2.13 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 PHE 0.016 0.002 PHE A 12 TYR 0.015 0.001 TYR A 269 ARG 0.006 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.359 Fit side-chains REVERT: A 12 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: A 17 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: A 178 TYR cc_start: 0.7896 (m-80) cc_final: 0.7551 (m-10) REVERT: A 324 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8000 (m-80) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1320 time to fit residues: 9.7522 Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.0470 chunk 24 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3897 Z= 0.191 Angle : 0.568 14.954 5313 Z= 0.270 Chirality : 0.038 0.173 636 Planarity : 0.004 0.041 644 Dihedral : 7.055 81.257 579 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.77 % Allowed : 18.14 % Favored : 79.09 % 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: 2.01 (0.41), residues: 495 helix: 2.18 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -1.41 (0.63), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 560 HIS 0.000 0.000 HIS A 226 PHE 0.016 0.001 PHE A 12 TYR 0.013 0.001 TYR A 269 ARG 0.006 0.000 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.437 Fit side-chains REVERT: A 12 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: A 17 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: A 23 MET cc_start: 0.7271 (tpp) cc_final: 0.6862 (ttm) REVERT: A 178 TYR cc_start: 0.7791 (m-80) cc_final: 0.7443 (m-10) REVERT: A 324 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7997 (m-80) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1371 time to fit residues: 10.1458 Evaluate side-chains 58 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112562 restraints weight = 5226.828| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.66 r_work: 0.3207 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3897 Z= 0.195 Angle : 0.583 14.879 5313 Z= 0.275 Chirality : 0.038 0.172 636 Planarity : 0.004 0.042 644 Dihedral : 6.973 80.523 579 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.52 % Allowed : 18.14 % Favored : 79.35 % 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: 2.01 (0.41), residues: 495 helix: 2.20 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.46 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 PHE 0.015 0.001 PHE A 12 TYR 0.013 0.001 TYR A 269 ARG 0.006 0.000 ARG A 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1199.26 seconds wall clock time: 21 minutes 55.52 seconds (1315.52 seconds total)