Starting phenix.real_space_refine on Fri Dec 27 10:13:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uuy_26806/12_2024/7uuy_26806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uuy_26806/12_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/cci-nas-00/data/ceres_data/7uuy_26806/12_2024/7uuy_26806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uuy_26806/12_2024/7uuy_26806.map" model { file = "/net/cci-nas-00/data/ceres_data/7uuy_26806/12_2024/7uuy_26806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uuy_26806/12_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. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.43, per 1000 atoms: 0.90 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 504.3 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: 0.44 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: 1.10 Time building geometry restraints manager: 1.32 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: 0.00 - 1.85: 5237 1.85 - 3.69: 59 3.69 - 5.54: 14 5.54 - 7.39: 1 7.39 - 9.23: 2 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 3.120 nonbonded pdb=" O HIS A 273 " pdb=" OG1 THR A 274 " model vdw 2.097 3.040 nonbonded pdb=" ND2 ASN A 441 " pdb=" O GLY A 546 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP A 311 " pdb=" OH TYR A 324 " model vdw 2.228 3.040 nonbonded pdb=" O HIS A 226 " pdb=" OG SER A 227 " model vdw 2.332 3.040 ... (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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.570 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.438 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: 0.1455 time to fit residues: 11.0242 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3897 Z= 0.254 Angle : 0.592 8.792 5313 Z= 0.297 Chirality : 0.040 0.160 636 Planarity : 0.005 0.047 644 Dihedral : 8.066 88.125 579 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.02 % Allowed : 9.82 % Favored : 88.16 % 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: 1.34 (0.41), residues: 495 helix: 1.65 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.30 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 559 HIS 0.001 0.001 HIS A 226 PHE 0.014 0.002 PHE A 12 TYR 0.016 0.002 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 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.429 Fit side-chains REVERT: A 516 ASP cc_start: 0.8006 (t0) cc_final: 0.7742 (t0) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1315 time to fit residues: 11.1071 Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3897 Z= 0.335 Angle : 0.601 6.810 5313 Z= 0.300 Chirality : 0.041 0.167 636 Planarity : 0.005 0.050 644 Dihedral : 7.882 89.917 579 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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: 1.38 (0.40), residues: 495 helix: 1.69 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.31 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.001 0.000 HIS A 226 PHE 0.029 0.002 PHE A 12 TYR 0.013 0.002 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 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.431 Fit side-chains REVERT: A 68 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7125 (tpp) REVERT: A 97 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.7721 (t0) REVERT: A 198 MET cc_start: 0.7042 (mtm) cc_final: 0.6664 (mtp) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.1475 time to fit residues: 10.5002 Evaluate side-chains 52 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.0020 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 43 optimal weight: 0.0870 chunk 13 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.2366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8067 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3897 Z= 0.184 Angle : 0.543 7.795 5313 Z= 0.269 Chirality : 0.038 0.206 636 Planarity : 0.004 0.044 644 Dihedral : 7.714 86.046 579 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 15.11 % 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: 1.76 (0.41), residues: 495 helix: 1.99 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.28 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 15 HIS 0.001 0.000 HIS A 226 PHE 0.040 0.002 PHE A 12 TYR 0.014 0.001 TYR A 269 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 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.340 Fit side-chains REVERT: A 11 THR cc_start: 0.8253 (m) cc_final: 0.7981 (p) REVERT: A 17 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: A 516 ASP cc_start: 0.7927 (t0) cc_final: 0.7599 (t0) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.1349 time to fit residues: 10.6697 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR 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: 0.9980 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8103 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3897 Z= 0.268 Angle : 0.559 7.034 5313 Z= 0.277 Chirality : 0.039 0.174 636 Planarity : 0.004 0.045 644 Dihedral : 7.484 84.494 579 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.76 % Allowed : 15.87 % Favored : 82.37 % 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: 1.72 (0.41), residues: 495 helix: 1.95 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.25 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.025 0.002 PHE A 12 TYR 0.012 0.001 TYR A 17 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 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.361 Fit side-chains REVERT: A 17 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: A 516 ASP cc_start: 0.7973 (t0) cc_final: 0.7582 (t0) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.1408 time to fit residues: 10.1137 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.0060 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8095 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3897 Z= 0.240 Angle : 0.547 6.434 5313 Z= 0.270 Chirality : 0.039 0.165 636 Planarity : 0.004 0.044 644 Dihedral : 7.330 81.839 579 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.52 % Allowed : 15.37 % Favored : 82.12 % 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: 1.72 (0.40), residues: 495 helix: 1.98 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.36 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.020 0.002 PHE A 12 TYR 0.012 0.001 TYR A 17 ARG 0.003 0.000 ARG A 228 *********************** 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 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.434 Fit side-chains REVERT: A 17 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: A 516 ASP cc_start: 0.7961 (t0) cc_final: 0.7556 (t0) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.1462 time to fit residues: 11.0613 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 167 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8082 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3897 Z= 0.221 Angle : 0.543 5.990 5313 Z= 0.271 Chirality : 0.038 0.159 636 Planarity : 0.004 0.043 644 Dihedral : 7.241 80.280 579 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.76 % Allowed : 16.62 % Favored : 81.61 % 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: 1.75 (0.41), residues: 495 helix: 2.11 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.53 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.036 0.002 PHE A 12 TYR 0.013 0.001 TYR A 17 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 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.432 Fit side-chains REVERT: A 11 THR cc_start: 0.8391 (m) cc_final: 0.8097 (p) REVERT: A 17 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: A 516 ASP cc_start: 0.8039 (t0) cc_final: 0.7615 (t0) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.1456 time to fit residues: 10.5356 Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.0000 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8076 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3897 Z= 0.221 Angle : 0.545 5.740 5313 Z= 0.272 Chirality : 0.038 0.149 636 Planarity : 0.004 0.043 644 Dihedral : 7.190 78.764 579 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.27 % Allowed : 16.88 % Favored : 80.86 % 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: 1.78 (0.41), residues: 495 helix: 2.15 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.54 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 PHE 0.028 0.002 PHE A 12 TYR 0.014 0.001 TYR A 17 ARG 0.004 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 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.443 Fit side-chains REVERT: A 17 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: A 23 MET cc_start: 0.7446 (tpp) cc_final: 0.7024 (ttm) REVERT: A 516 ASP cc_start: 0.8023 (t0) cc_final: 0.7597 (t0) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.1399 time to fit residues: 10.1407 Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8095 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3897 Z= 0.261 Angle : 0.597 15.065 5313 Z= 0.287 Chirality : 0.039 0.151 636 Planarity : 0.004 0.043 644 Dihedral : 7.061 77.396 579 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.76 % Allowed : 17.88 % Favored : 80.35 % 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: 1.72 (0.40), residues: 495 helix: 2.11 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.59 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 PHE 0.029 0.002 PHE A 12 TYR 0.013 0.001 TYR A 17 ARG 0.003 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 52 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.427 Fit side-chains REVERT: A 17 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: A 23 MET cc_start: 0.7377 (tpp) cc_final: 0.6945 (ttm) REVERT: A 516 ASP cc_start: 0.8055 (t0) cc_final: 0.7628 (t0) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.1456 time to fit residues: 9.3918 Evaluate side-chains 52 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET 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: 0.5980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8070 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3897 Z= 0.212 Angle : 0.582 14.797 5313 Z= 0.278 Chirality : 0.038 0.153 636 Planarity : 0.004 0.043 644 Dihedral : 6.734 76.257 579 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.76 % Allowed : 18.14 % 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: 1.74 (0.41), residues: 495 helix: 2.05 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 226 PHE 0.025 0.002 PHE A 12 TYR 0.013 0.001 TYR A 17 ARG 0.003 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 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.438 Fit side-chains REVERT: A 17 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: A 23 MET cc_start: 0.7300 (tpp) cc_final: 0.6887 (ttm) REVERT: A 68 MET cc_start: 0.6212 (tpp) cc_final: 0.5952 (tpt) REVERT: A 516 ASP cc_start: 0.8009 (t0) cc_final: 0.7620 (t0) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.1431 time to fit residues: 9.8639 Evaluate side-chains 53 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET 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: 0.0570 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111414 restraints weight = 5274.314| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.66 r_work: 0.3181 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3897 Z= 0.209 Angle : 0.571 14.772 5313 Z= 0.273 Chirality : 0.038 0.149 636 Planarity : 0.004 0.042 644 Dihedral : 6.576 75.604 579 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.76 % Allowed : 18.64 % 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: 1.78 (0.41), residues: 495 helix: 2.17 (0.28), residues: 361 sheet: None (None), residues: 0 loop : -1.69 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 PHE 0.024 0.002 PHE A 12 TYR 0.013 0.001 TYR A 17 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: 1223.54 seconds wall clock time: 22 minutes 49.47 seconds (1369.47 seconds total)