Starting phenix.real_space_refine on Sun Mar 10 15:01:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/03_2024/8dly_27520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/03_2024/8dly_27520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/03_2024/8dly_27520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/03_2024/8dly_27520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dly_27520/03_2024/8dly_27520.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 1.88, per 1000 atoms: 0.76 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 457.5 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: 0.58 Time building geometry restraints manager: 1.05 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: 100.44 - 107.16: 85 107.16 - 113.88: 1306 113.88 - 120.59: 1034 120.59 - 127.31: 1011 127.31 - 134.02: 33 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 2.440 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.432 2.520 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.487 2.520 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.505 2.440 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.524 2.440 ... (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 ========== 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: 2.600 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: 12.890 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.070 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.288 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: 1.1416 time to fit residues: 116.6609 Evaluate side-chains 63 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 0.0870 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2550 Z= 0.155 Angle : 0.572 6.007 3469 Z= 0.283 Chirality : 0.043 0.134 370 Planarity : 0.004 0.032 448 Dihedral : 6.407 53.203 377 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.12 % Allowed : 16.85 % Favored : 79.03 % 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 (0.41), residues: 310 helix: -3.52 (0.73), residues: 26 sheet: 0.15 (0.48), residues: 98 loop : -0.59 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS C 519 PHE 0.005 0.001 PHE H 27 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 85 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8403 (ptm-80) cc_final: 0.8142 (ptm-80) REVERT: C 420 ASP cc_start: 0.8539 (m-30) cc_final: 0.8284 (m-30) REVERT: C 424 LYS cc_start: 0.8834 (tptt) cc_final: 0.8617 (tppp) REVERT: C 456 PHE cc_start: 0.8649 (t80) cc_final: 0.8274 (t80) REVERT: H 60 ASN cc_start: 0.8808 (t0) cc_final: 0.8599 (t0) REVERT: H 86 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6561 (mtp180) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 1.1718 time to fit residues: 95.9597 Evaluate side-chains 67 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 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 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: 1.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8067 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2550 Z= 0.249 Angle : 0.603 6.465 3469 Z= 0.302 Chirality : 0.044 0.138 370 Planarity : 0.004 0.032 448 Dihedral : 5.495 45.767 375 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.62 % Allowed : 19.48 % Favored : 74.91 % 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: -1.04 (0.43), residues: 310 helix: -3.36 (0.87), residues: 26 sheet: 0.14 (0.47), residues: 103 loop : -0.73 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE C 347 TYR 0.011 0.001 TYR C 495 ARG 0.008 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 81 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8506 (m-30) cc_final: 0.8236 (m-30) REVERT: C 424 LYS cc_start: 0.8906 (tptt) cc_final: 0.8694 (tppp) REVERT: C 444 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8219 (mtmm) REVERT: C 493 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: H 60 ASN cc_start: 0.8902 (t0) cc_final: 0.8693 (t0) REVERT: H 74 SER cc_start: 0.9140 (m) cc_final: 0.8900 (t) REVERT: H 86 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6651 (mtp180) REVERT: H 88 GLU cc_start: 0.8786 (pp20) cc_final: 0.8485 (pp20) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 1.1828 time to fit residues: 89.5220 Evaluate side-chains 70 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 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 492 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL 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: 0.5980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2550 Z= 0.327 Angle : 0.624 7.418 3469 Z= 0.312 Chirality : 0.045 0.134 370 Planarity : 0.004 0.031 448 Dihedral : 5.897 53.733 373 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.62 % Allowed : 20.22 % Favored : 74.16 % 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: -1.25 (0.44), residues: 310 helix: -3.01 (1.02), residues: 26 sheet: -0.08 (0.46), residues: 110 loop : -0.93 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE C 347 TYR 0.012 0.001 TYR C 495 ARG 0.008 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 79 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8439 (m-30) cc_final: 0.8201 (m-30) REVERT: C 424 LYS cc_start: 0.8876 (tptt) cc_final: 0.8577 (tppp) REVERT: C 444 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8195 (mtmm) REVERT: C 493 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: H 29 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7126 (t80) REVERT: H 39 GLN cc_start: 0.7943 (pt0) cc_final: 0.7501 (tt0) REVERT: H 74 SER cc_start: 0.9160 (m) cc_final: 0.8937 (t) REVERT: H 86 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6615 (mtp180) REVERT: H 88 GLU cc_start: 0.8757 (pp20) cc_final: 0.8371 (pp20) outliers start: 15 outliers final: 6 residues processed: 74 average time/residue: 1.2314 time to fit residues: 93.1131 Evaluate side-chains 78 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 493 GLN 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: 2.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 2550 Z= 0.309 Angle : 0.602 7.120 3469 Z= 0.305 Chirality : 0.044 0.133 370 Planarity : 0.004 0.028 448 Dihedral : 5.828 54.518 373 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.99 % Allowed : 20.97 % Favored : 73.03 % 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: -1.30 (0.43), residues: 310 helix: -2.92 (1.03), residues: 26 sheet: -0.20 (0.45), residues: 110 loop : -0.92 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE C 347 TYR 0.013 0.001 TYR H 101 ARG 0.007 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 84 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 414 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8500 (mm-40) REVERT: C 424 LYS cc_start: 0.8891 (tptt) cc_final: 0.8557 (tppp) REVERT: C 444 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8214 (mtmm) REVERT: C 493 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: H 29 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6883 (t80) REVERT: H 39 GLN cc_start: 0.7980 (pt0) cc_final: 0.7560 (tt0) REVERT: H 74 SER cc_start: 0.9161 (m) cc_final: 0.8933 (t) REVERT: H 86 ARG cc_start: 0.7024 (mtp180) cc_final: 0.6630 (mtp180) REVERT: H 88 GLU cc_start: 0.8809 (pp20) cc_final: 0.8375 (pp20) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 1.1451 time to fit residues: 92.6243 Evaluate side-chains 74 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 492 LEU Chi-restraints excluded: chain C residue 493 GLN 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 Chi-restraints excluded: chain H residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8074 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2550 Z= 0.186 Angle : 0.578 5.999 3469 Z= 0.287 Chirality : 0.043 0.131 370 Planarity : 0.004 0.035 448 Dihedral : 5.408 50.799 373 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.37 % Allowed : 20.97 % Favored : 72.66 % 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: -1.20 (0.44), residues: 310 helix: -3.14 (1.12), residues: 20 sheet: -0.27 (0.46), residues: 110 loop : -0.81 (0.42), residues: 180 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 0.005 0.001 PHE C 347 TYR 0.009 0.001 TYR H 79 ARG 0.008 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 fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8449 (ttp80) REVERT: C 424 LYS cc_start: 0.8888 (tptt) cc_final: 0.8562 (tppp) REVERT: C 444 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: C 516 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6464 (tm-30) REVERT: H 39 GLN cc_start: 0.7887 (pt0) cc_final: 0.7496 (tt0) REVERT: H 74 SER cc_start: 0.9134 (m) cc_final: 0.8919 (t) REVERT: H 86 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6643 (mtp180) REVERT: H 88 GLU cc_start: 0.8842 (pp20) cc_final: 0.8409 (pp20) outliers start: 17 outliers final: 10 residues processed: 75 average time/residue: 1.2598 time to fit residues: 96.4648 Evaluate side-chains 71 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 73 ASP 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: 0.6980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 11 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2550 Z= 0.177 Angle : 0.588 6.339 3469 Z= 0.294 Chirality : 0.044 0.132 370 Planarity : 0.004 0.036 448 Dihedral : 5.190 46.700 373 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.99 % Allowed : 21.72 % Favored : 72.28 % 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: -3.12 (1.09), residues: 20 sheet: -0.13 (0.47), residues: 108 loop : -0.76 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS H 35 PHE 0.005 0.001 PHE C 515 TYR 0.014 0.001 TYR H 101 ARG 0.008 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 85 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8454 (ttp80) REVERT: C 420 ASP cc_start: 0.8367 (m-30) cc_final: 0.7950 (m-30) REVERT: C 424 LYS cc_start: 0.8899 (tptt) cc_final: 0.8574 (tppp) REVERT: C 444 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8223 (mtmm) REVERT: C 516 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6487 (tm-30) REVERT: C 523 THR cc_start: 0.8504 (p) cc_final: 0.8236 (t) REVERT: H 39 GLN cc_start: 0.7863 (pt0) cc_final: 0.7471 (tt0) REVERT: H 74 SER cc_start: 0.9132 (m) cc_final: 0.8932 (t) REVERT: H 86 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6624 (mtp180) REVERT: H 88 GLU cc_start: 0.8792 (pp20) cc_final: 0.8344 (pp20) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 1.1729 time to fit residues: 93.6224 Evaluate side-chains 76 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 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 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 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 27 PHE Chi-restraints excluded: chain H residue 73 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2550 Z= 0.258 Angle : 0.599 6.623 3469 Z= 0.302 Chirality : 0.044 0.134 370 Planarity : 0.004 0.037 448 Dihedral : 5.357 48.620 373 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.24 % Allowed : 23.60 % Favored : 71.16 % 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: -1.19 (0.45), residues: 310 helix: -2.87 (0.98), residues: 26 sheet: -0.16 (0.47), residues: 108 loop : -0.82 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 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 0.009 0.001 ARG H 16 *********************** 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 80 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8508 (ttp80) REVERT: C 414 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8577 (mm-40) REVERT: C 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.7922 (m-30) REVERT: C 424 LYS cc_start: 0.8895 (tptt) cc_final: 0.8570 (tppp) REVERT: C 444 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8229 (mtmm) REVERT: C 516 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6519 (tm-30) REVERT: C 523 THR cc_start: 0.8586 (p) cc_final: 0.8347 (t) REVERT: H 39 GLN cc_start: 0.7932 (pt0) cc_final: 0.7533 (tt0) REVERT: H 86 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6695 (mtp180) REVERT: H 88 GLU cc_start: 0.8779 (pp20) cc_final: 0.8334 (pp20) outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 1.1782 time to fit residues: 89.1613 Evaluate side-chains 74 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 73 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.0010 chunk 14 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3994 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= 0.168 Angle : 0.593 7.090 3469 Z= 0.295 Chirality : 0.044 0.132 370 Planarity : 0.004 0.036 448 Dihedral : 4.948 42.757 373 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.62 % Allowed : 24.72 % 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: -0.95 (0.45), residues: 310 helix: -2.99 (1.13), residues: 20 sheet: -0.08 (0.48), residues: 106 loop : -0.64 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.005 0.001 PHE C 515 TYR 0.011 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 89 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: C 414 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8589 (mm-40) REVERT: C 420 ASP cc_start: 0.8382 (m-30) cc_final: 0.8056 (m-30) REVERT: C 424 LYS cc_start: 0.8888 (tptt) cc_final: 0.8678 (tppp) REVERT: C 444 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: C 516 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6546 (tm-30) REVERT: H 39 GLN cc_start: 0.7862 (pt0) cc_final: 0.7480 (tt0) REVERT: H 73 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8643 (m-30) REVERT: H 86 ARG cc_start: 0.6965 (mtp180) cc_final: 0.6652 (mtp180) REVERT: H 88 GLU cc_start: 0.8790 (pp20) cc_final: 0.8317 (pp20) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 1.2267 time to fit residues: 102.7652 Evaluate side-chains 78 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 12 VAL Chi-restraints excluded: chain H residue 73 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2550 Z= 0.220 Angle : 0.640 8.911 3469 Z= 0.315 Chirality : 0.044 0.135 370 Planarity : 0.004 0.035 448 Dihedral : 5.034 43.400 373 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.24 % Allowed : 24.72 % 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: -1.03 (0.45), residues: 310 helix: -2.85 (1.21), residues: 20 sheet: -0.18 (0.48), residues: 106 loop : -0.69 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.017 0.001 PHE C 392 TYR 0.011 0.001 TYR H 79 ARG 0.009 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 83 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 414 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8632 (mm-40) REVERT: C 420 ASP cc_start: 0.8399 (m-30) cc_final: 0.8071 (m-30) REVERT: C 424 LYS cc_start: 0.8882 (tptt) cc_final: 0.8672 (tppp) REVERT: C 444 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8238 (mtmm) REVERT: C 516 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6445 (tm-30) REVERT: H 39 GLN cc_start: 0.7911 (pt0) cc_final: 0.7519 (tt0) REVERT: H 86 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6691 (mtp180) REVERT: H 88 GLU cc_start: 0.8779 (pp20) cc_final: 0.8320 (pp20) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 1.1795 time to fit residues: 91.6512 Evaluate side-chains 75 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074740 restraints weight = 5771.714| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.12 r_work: 0.3052 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2550 Z= 0.227 Angle : 0.663 9.030 3469 Z= 0.325 Chirality : 0.045 0.168 370 Planarity : 0.004 0.035 448 Dihedral : 5.079 43.635 373 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.24 % Allowed : 25.84 % Favored : 68.91 % 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: -2.81 (1.23), residues: 20 sheet: -0.19 (0.48), residues: 108 loop : -0.67 (0.43), residues: 182 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 0.006 0.001 PHE C 515 TYR 0.014 0.001 TYR H 101 ARG 0.009 0.001 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.88 seconds wall clock time: 36 minutes 51.59 seconds (2211.59 seconds total)