Starting phenix.real_space_refine on Fri Dec 27 05:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dly_27520/12_2024/8dly_27520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/12_2024/8dly_27520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/12_2024/8dly_27520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/12_2024/8dly_27520.map" model { file = "/net/cci-nas-00/data/ceres_data/8dly_27520/12_2024/8dly_27520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/12_2024/8dly_27520.cif" } resolution = 3.0 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= -0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1582 2.51 5 N 417 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2483 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.08, per 1000 atoms: 1.24 Number of scatterers: 2483 At special positions: 0 Unit cell: (68, 82, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 471 8.00 N 417 7.00 C 1582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 340.3 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.619A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.081A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.330A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.505A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.660A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.815A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.124A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 186 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: 0.59 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 783 1.34 - 1.46: 649 1.46 - 1.58: 1102 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2550 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" CB ASN H 50 " pdb=" CG ASN H 50 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.19e-02 7.06e+03 2.32e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3270 1.92 - 3.84: 172 3.84 - 5.76: 21 5.76 - 7.68: 4 7.68 - 9.60: 2 Bond angle restraints: 3469 Sorted by residual: angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" C GLY C 476 " pdb=" N SER C 477 " pdb=" CA SER C 477 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.78e+00 angle pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta sigma weight residual 120.38 124.48 -4.10 1.37e+00 5.33e-01 8.95e+00 angle pdb=" N LEU C 518 " pdb=" CA LEU C 518 " pdb=" C LEU C 518 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 125.90 -9.60 3.50e+00 8.16e-02 7.52e+00 ... (remaining 3464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 1306 13.75 - 27.50: 146 27.50 - 41.25: 38 41.25 - 54.99: 9 54.99 - 68.74: 1 Dihedral angle restraints: 1500 sinusoidal: 593 harmonic: 907 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 126.09 -33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual 180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CG ARG C 509 " pdb=" CD ARG C 509 " pdb=" NE ARG C 509 " pdb=" CZ ARG C 509 " ideal model delta sinusoidal sigma weight residual -90.00 -131.99 41.99 2 1.50e+01 4.44e-03 9.55e+00 ... (remaining 1497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 224 0.046 - 0.093: 100 0.093 - 0.139: 38 0.139 - 0.185: 5 0.185 - 0.231: 3 Chirality restraints: 370 Sorted by residual: chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA MET H 106 " pdb=" N MET H 106 " pdb=" C MET H 106 " pdb=" CB MET H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 367 not shown) Planarity restraints: 449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 520 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA C 520 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 520 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO C 521 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN H 60 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO H 61 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 41 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.025 5.00e-02 4.00e+02 ... (remaining 446 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 789 2.83 - 3.35: 1927 3.35 - 3.87: 4036 3.87 - 4.38: 4493 4.38 - 4.90: 8057 Nonbonded interactions: 19302 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.317 3.040 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.432 3.120 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.487 3.120 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.505 3.040 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.524 3.040 ... (remaining 19297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.005 0.051 2550 Z= 0.329 Angle : 0.939 9.601 3469 Z= 0.512 Chirality : 0.059 0.231 370 Planarity : 0.006 0.053 448 Dihedral : 12.405 68.742 913 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.37 % Allowed : 3.00 % Favored : 96.63 % 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: -1.46 (0.40), residues: 310 helix: -3.94 (0.60), residues: 26 sheet: -0.08 (0.45), residues: 104 loop : -1.03 (0.37), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 47 HIS 0.011 0.003 HIS H 35 PHE 0.017 0.002 PHE H 27 TYR 0.015 0.002 TYR C 453 ARG 0.007 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.250 Fit side-chains REVERT: C 420 ASP cc_start: 0.8522 (m-30) cc_final: 0.8206 (m-30) REVERT: C 424 LYS cc_start: 0.8840 (tptt) cc_final: 0.8594 (tppp) REVERT: C 456 PHE cc_start: 0.8663 (t80) cc_final: 0.8216 (t80) REVERT: C 474 GLN cc_start: 0.7637 (mt0) cc_final: 0.7419 (mt0) REVERT: H 39 GLN cc_start: 0.7728 (pt0) cc_final: 0.7151 (pm20) REVERT: H 86 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6622 (mtp180) REVERT: H 92 ILE cc_start: 0.8541 (mt) cc_final: 0.7759 (mm) outliers start: 1 outliers final: 2 residues processed: 100 average time/residue: 1.1649 time to fit residues: 119.0033 Evaluate side-chains 63 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN C 506 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2550 Z= 0.187 Angle : 0.596 6.518 3469 Z= 0.295 Chirality : 0.044 0.140 370 Planarity : 0.004 0.032 448 Dihedral : 8.726 124.730 377 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.75 % Allowed : 16.85 % Favored : 79.40 % 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: -0.97 (0.42), residues: 310 helix: -3.58 (0.75), residues: 26 sheet: 0.11 (0.48), residues: 98 loop : -0.56 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS C 519 PHE 0.006 0.001 PHE H 29 TYR 0.014 0.001 TYR H 79 ARG 0.005 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8414 (ptm-80) cc_final: 0.8158 (ptm-80) REVERT: C 420 ASP cc_start: 0.8537 (m-30) cc_final: 0.8270 (m-30) REVERT: C 424 LYS cc_start: 0.8949 (tptt) cc_final: 0.8739 (tppp) REVERT: C 456 PHE cc_start: 0.8655 (t80) cc_final: 0.8271 (t80) REVERT: H 29 PHE cc_start: 0.8380 (t80) cc_final: 0.8112 (t80) REVERT: H 60 ASN cc_start: 0.8908 (t0) cc_final: 0.8688 (t0) REVERT: H 86 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6578 (mtp180) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 1.2510 time to fit residues: 99.6842 Evaluate side-chains 69 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2550 Z= 0.206 Angle : 0.582 6.493 3469 Z= 0.293 Chirality : 0.043 0.137 370 Planarity : 0.004 0.031 448 Dihedral : 5.242 43.362 375 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.62 % Allowed : 18.73 % Favored : 75.66 % 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: -0.98 (0.43), residues: 310 helix: -3.49 (1.03), residues: 20 sheet: 0.13 (0.47), residues: 103 loop : -0.75 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.007 0.001 PHE C 347 TYR 0.009 0.001 TYR C 495 ARG 0.007 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8478 (m-30) cc_final: 0.8183 (m-30) REVERT: C 424 LYS cc_start: 0.8944 (tptt) cc_final: 0.8726 (tppp) REVERT: C 444 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: H 86 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6689 (mtp180) REVERT: H 88 GLU cc_start: 0.8813 (pp20) cc_final: 0.8531 (pp20) outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 1.1448 time to fit residues: 93.6086 Evaluate side-chains 69 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2550 Z= 0.310 Angle : 0.619 6.931 3469 Z= 0.307 Chirality : 0.045 0.138 370 Planarity : 0.004 0.035 448 Dihedral : 5.484 47.826 373 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.62 % Allowed : 19.85 % Favored : 74.53 % 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: -1.09 (0.44), residues: 310 helix: -3.10 (0.98), residues: 26 sheet: 0.02 (0.46), residues: 110 loop : -0.79 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.028 0.002 PHE H 27 TYR 0.012 0.001 TYR C 495 ARG 0.010 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8459 (m-30) cc_final: 0.8176 (m-30) REVERT: C 424 LYS cc_start: 0.8950 (tptt) cc_final: 0.8661 (tppp) REVERT: C 444 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: H 29 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7208 (t80) REVERT: H 74 SER cc_start: 0.9132 (m) cc_final: 0.8880 (t) REVERT: H 86 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6649 (mtp180) REVERT: H 88 GLU cc_start: 0.8772 (pp20) cc_final: 0.8396 (pp20) REVERT: H 89 ASP cc_start: 0.7839 (m-30) cc_final: 0.7627 (m-30) outliers start: 15 outliers final: 6 residues processed: 75 average time/residue: 1.2182 time to fit residues: 93.4092 Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2550 Z= 0.310 Angle : 0.620 7.754 3469 Z= 0.310 Chirality : 0.044 0.138 370 Planarity : 0.004 0.032 448 Dihedral : 5.473 47.931 373 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.37 % Allowed : 20.22 % Favored : 73.41 % 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: -1.22 (0.44), residues: 310 helix: -3.05 (0.98), residues: 26 sheet: -0.13 (0.46), residues: 110 loop : -0.85 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.026 0.001 PHE H 27 TYR 0.013 0.001 TYR H 101 ARG 0.008 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8481 (ttm-80) REVERT: C 420 ASP cc_start: 0.8429 (m-30) cc_final: 0.8129 (m-30) REVERT: C 424 LYS cc_start: 0.8932 (tptt) cc_final: 0.8673 (tppp) REVERT: C 444 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8230 (mtmm) REVERT: C 516 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6471 (tm-30) REVERT: H 29 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7156 (t80) REVERT: H 39 GLN cc_start: 0.7878 (pt0) cc_final: 0.7409 (tt0) REVERT: H 74 SER cc_start: 0.9168 (m) cc_final: 0.8930 (t) REVERT: H 86 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6635 (mtp180) REVERT: H 88 GLU cc_start: 0.8778 (pp20) cc_final: 0.8350 (pp20) outliers start: 17 outliers final: 10 residues processed: 75 average time/residue: 1.1994 time to fit residues: 92.0214 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2550 Z= 0.237 Angle : 0.612 6.994 3469 Z= 0.305 Chirality : 0.044 0.135 370 Planarity : 0.004 0.028 448 Dihedral : 5.343 45.747 373 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.37 % Allowed : 22.10 % Favored : 71.54 % 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: -1.19 (0.44), residues: 310 helix: -2.99 (0.98), residues: 26 sheet: -0.27 (0.45), residues: 110 loop : -0.71 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.022 0.001 PHE H 27 TYR 0.010 0.001 TYR C 495 ARG 0.007 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8442 (ttp80) REVERT: C 420 ASP cc_start: 0.8419 (m-30) cc_final: 0.8201 (m-30) REVERT: C 424 LYS cc_start: 0.8939 (tptt) cc_final: 0.8682 (tppp) REVERT: C 444 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: C 516 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6738 (tm-30) REVERT: H 39 GLN cc_start: 0.7858 (pt0) cc_final: 0.7395 (tt0) REVERT: H 74 SER cc_start: 0.9155 (m) cc_final: 0.8927 (t) REVERT: H 86 ARG cc_start: 0.6939 (mtp180) cc_final: 0.6617 (mtp180) REVERT: H 88 GLU cc_start: 0.8822 (pp20) cc_final: 0.8374 (pp20) REVERT: H 89 ASP cc_start: 0.7837 (m-30) cc_final: 0.7626 (m-30) outliers start: 17 outliers final: 9 residues processed: 72 average time/residue: 1.2399 time to fit residues: 91.2387 Evaluate side-chains 73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2550 Z= 0.186 Angle : 0.621 7.445 3469 Z= 0.305 Chirality : 0.044 0.135 370 Planarity : 0.004 0.036 448 Dihedral : 4.998 40.993 373 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.87 % Allowed : 23.60 % Favored : 71.54 % 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: -0.96 (0.44), residues: 310 helix: -3.06 (1.13), residues: 20 sheet: -0.15 (0.47), residues: 102 loop : -0.59 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.021 0.001 PHE H 27 TYR 0.013 0.001 TYR H 101 ARG 0.009 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8161 (ptm-80) REVERT: C 424 LYS cc_start: 0.8954 (tptt) cc_final: 0.8694 (tppp) REVERT: C 444 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8181 (mtmm) REVERT: C 516 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6766 (tm-30) REVERT: C 523 THR cc_start: 0.8448 (p) cc_final: 0.8165 (t) REVERT: H 39 GLN cc_start: 0.7851 (pt0) cc_final: 0.7427 (tt0) REVERT: H 74 SER cc_start: 0.9115 (m) cc_final: 0.8899 (t) REVERT: H 86 ARG cc_start: 0.6879 (mtp180) cc_final: 0.6588 (mtp180) REVERT: H 88 GLU cc_start: 0.8855 (pp20) cc_final: 0.8436 (pp20) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 1.2027 time to fit residues: 94.6820 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2550 Z= 0.280 Angle : 0.642 8.743 3469 Z= 0.317 Chirality : 0.044 0.137 370 Planarity : 0.004 0.040 448 Dihedral : 5.231 45.191 373 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.62 % Allowed : 23.97 % Favored : 70.41 % 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: -1.17 (0.45), residues: 310 helix: -2.74 (1.04), residues: 26 sheet: -0.36 (0.46), residues: 104 loop : -0.65 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE H 27 TYR 0.010 0.001 TYR C 495 ARG 0.009 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8448 (ttp80) REVERT: C 408 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.8196 (ptm-80) REVERT: C 424 LYS cc_start: 0.8944 (tptt) cc_final: 0.8663 (tppp) REVERT: C 444 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: C 516 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6751 (tm-30) REVERT: H 39 GLN cc_start: 0.7915 (pt0) cc_final: 0.7454 (tt0) REVERT: H 74 SER cc_start: 0.9166 (m) cc_final: 0.8943 (t) REVERT: H 86 ARG cc_start: 0.7026 (mtp180) cc_final: 0.6670 (mtp180) REVERT: H 88 GLU cc_start: 0.8816 (pp20) cc_final: 0.8383 (pp20) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 1.2319 time to fit residues: 93.1245 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.0040 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 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: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2550 Z= 0.212 Angle : 0.625 8.250 3469 Z= 0.309 Chirality : 0.044 0.142 370 Planarity : 0.004 0.034 448 Dihedral : 5.041 42.466 373 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.24 % Allowed : 24.34 % Favored : 70.41 % 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: -1.02 (0.45), residues: 310 helix: -2.76 (1.23), residues: 20 sheet: -0.28 (0.47), residues: 102 loop : -0.61 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE H 27 TYR 0.012 0.001 TYR H 101 ARG 0.008 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8398 (ttp80) REVERT: C 408 ARG cc_start: 0.8416 (ptm-80) cc_final: 0.8198 (ptm-80) REVERT: C 420 ASP cc_start: 0.8276 (m-30) cc_final: 0.7884 (m-30) REVERT: C 424 LYS cc_start: 0.8946 (tptt) cc_final: 0.8664 (tppp) REVERT: C 444 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: C 516 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6704 (tm-30) REVERT: C 523 THR cc_start: 0.8526 (p) cc_final: 0.8284 (t) REVERT: H 39 GLN cc_start: 0.7872 (pt0) cc_final: 0.7440 (tt0) REVERT: H 86 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6637 (mtp180) REVERT: H 88 GLU cc_start: 0.8815 (pp20) cc_final: 0.8381 (pp20) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 1.2251 time to fit residues: 95.1829 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2550 Z= 0.185 Angle : 0.620 8.673 3469 Z= 0.305 Chirality : 0.043 0.135 370 Planarity : 0.004 0.033 448 Dihedral : 4.791 39.493 373 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.49 % Allowed : 25.47 % Favored : 70.04 % 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: -1.02 (0.45), residues: 310 helix: -2.70 (1.23), residues: 20 sheet: -0.34 (0.47), residues: 102 loop : -0.57 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.019 0.001 PHE H 27 TYR 0.009 0.001 TYR H 79 ARG 0.008 0.001 ARG H 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.8201 (ptm-80) REVERT: C 420 ASP cc_start: 0.8206 (m-30) cc_final: 0.7792 (m-30) REVERT: C 424 LYS cc_start: 0.8951 (tptt) cc_final: 0.8670 (tppp) REVERT: C 444 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8195 (mtmm) REVERT: C 516 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6744 (tm-30) REVERT: C 517 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7372 (mm) REVERT: H 39 GLN cc_start: 0.7847 (pt0) cc_final: 0.7458 (tt0) REVERT: H 86 ARG cc_start: 0.6977 (mtp180) cc_final: 0.6587 (mtp180) REVERT: H 88 GLU cc_start: 0.8821 (pp20) cc_final: 0.8368 (pp20) outliers start: 12 outliers final: 7 residues processed: 75 average time/residue: 1.2763 time to fit residues: 97.7143 Evaluate side-chains 70 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074469 restraints weight = 5810.627| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.19 r_work: 0.3077 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2550 Z= 0.210 Angle : 0.640 8.787 3469 Z= 0.316 Chirality : 0.044 0.137 370 Planarity : 0.004 0.041 448 Dihedral : 4.826 40.076 373 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.12 % Allowed : 26.22 % Favored : 69.66 % 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: -1.02 (0.45), residues: 310 helix: -2.66 (1.25), residues: 20 sheet: -0.33 (0.47), residues: 102 loop : -0.58 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.001 0.001 HIS H 35 PHE 0.018 0.001 PHE H 27 TYR 0.014 0.001 TYR H 101 ARG 0.010 0.001 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.75 seconds wall clock time: 37 minutes 38.66 seconds (2258.66 seconds total)