Starting phenix.real_space_refine on Mon Feb 10 20:03:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzu_22574/02_2025/7jzu_22574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzu_22574/02_2025/7jzu_22574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzu_22574/02_2025/7jzu_22574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzu_22574/02_2025/7jzu_22574.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzu_22574/02_2025/7jzu_22574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzu_22574/02_2025/7jzu_22574.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 11 5.16 5 C 1270 2.51 5 N 325 2.21 5 O 381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1987 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1512 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.64, per 1000 atoms: 1.33 Number of scatterers: 1987 At special positions: 0 Unit cell: (59.85, 71.4, 66.15, 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 11 16.00 O 381 8.00 N 325 7.00 C 1270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.16 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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 BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN B 343 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 236.2 milliseconds 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 36.7% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.566A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.781A pdb=" N LEU A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 removed outlier: 4.251A pdb=" N GLU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.716A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.979A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.459A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.944A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.591A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 80 hydrogen bonds defined for protein. 204 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: 0.44 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 571 1.33 - 1.46: 603 1.46 - 1.59: 846 1.59 - 1.73: 0 1.73 - 1.86: 14 Bond restraints: 2034 Sorted by residual: bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ASN B 487 " pdb=" CG ASN B 487 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.85e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.03e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.476 -0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 2029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 2134 1.42 - 2.85: 499 2.85 - 4.27: 87 4.27 - 5.70: 31 5.70 - 7.12: 9 Bond angle restraints: 2760 Sorted by residual: angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.07 -6.51 1.02e+00 9.61e-01 4.08e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.95 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C LEU B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta sigma weight residual 120.03 126.20 -6.17 9.90e-01 1.02e+00 3.89e+01 angle pdb=" C THR B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta sigma weight residual 119.78 126.05 -6.27 1.03e+00 9.43e-01 3.71e+01 angle pdb=" C ALA B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 119.76 125.81 -6.05 1.03e+00 9.43e-01 3.45e+01 ... (remaining 2755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 1169 13.82 - 27.64: 52 27.64 - 41.46: 17 41.46 - 55.27: 4 55.27 - 69.09: 2 Dihedral angle restraints: 1244 sinusoidal: 519 harmonic: 725 Sorted by residual: dihedral pdb=" C TYR B 495 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta harmonic sigma weight residual -122.60 -114.96 -7.64 0 2.50e+00 1.60e-01 9.34e+00 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 116.81 -23.81 1 1.00e+01 1.00e-02 8.17e+00 dihedral pdb=" CB GLU B 484 " pdb=" CG GLU B 484 " pdb=" CD GLU B 484 " pdb=" OE1 GLU B 484 " ideal model delta sinusoidal sigma weight residual 0.00 69.09 -69.09 1 3.00e+01 1.11e-03 6.86e+00 ... (remaining 1241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 199 0.074 - 0.149: 81 0.149 - 0.223: 18 0.223 - 0.298: 4 0.298 - 0.372: 2 Chirality restraints: 304 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.72e+01 chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.21e+01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.86 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 301 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.043 2.00e-02 2.50e+03 2.19e-02 9.57e+00 pdb=" CG TYR B 495 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " 0.025 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR B 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 505 " -0.026 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 505 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 505 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 505 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 505 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 505 " -0.023 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1044 2.99 - 3.47: 1816 3.47 - 3.94: 3369 3.94 - 4.42: 3931 4.42 - 4.90: 6085 Nonbonded interactions: 16245 Sorted by model distance: nonbonded pdb=" N ALA B 520 " pdb=" O ALA B 520 " model vdw 2.509 2.496 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.573 3.120 nonbonded pdb=" N ASN B 440 " pdb=" OD1 ASN B 440 " model vdw 2.586 3.120 nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.597 2.496 nonbonded pdb=" N GLN B 506 " pdb=" O GLN B 506 " model vdw 2.617 2.496 ... (remaining 16240 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.870 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 : 0.015 0.074 2034 Z= 0.953 Angle : 1.344 7.124 2760 Z= 0.904 Chirality : 0.085 0.372 304 Planarity : 0.005 0.022 355 Dihedral : 9.379 69.093 770 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.23 (0.52), residues: 244 helix: -1.00 (0.53), residues: 78 sheet: 0.98 (0.75), residues: 49 loop : 0.87 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP B 353 HIS 0.002 0.001 HIS A 21 PHE 0.014 0.003 PHE B 497 TYR 0.043 0.006 TYR B 495 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.231 Fit side-chains REVERT: B 361 CYS cc_start: 0.6296 (p) cc_final: 0.5724 (p) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1700 time to fit residues: 9.4562 Evaluate side-chains 32 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 487 ASN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.157598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144611 restraints weight = 2305.090| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.13 r_work: 0.3496 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2034 Z= 0.277 Angle : 0.606 7.138 2760 Z= 0.314 Chirality : 0.045 0.165 304 Planarity : 0.004 0.041 355 Dihedral : 4.365 15.505 334 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 4.41 % Favored : 93.63 % 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: 0.51 (0.54), residues: 244 helix: -0.07 (0.61), residues: 75 sheet: 0.55 (0.77), residues: 48 loop : 0.75 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.005 0.003 HIS A 21 PHE 0.014 0.002 PHE B 497 TYR 0.026 0.002 TYR B 495 ARG 0.003 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.268 Fit side-chains REVERT: A 13 MET cc_start: 0.8471 (ptm) cc_final: 0.8056 (ptt) REVERT: A 29 SER cc_start: 0.8277 (t) cc_final: 0.7813 (p) REVERT: B 361 CYS cc_start: 0.7400 (p) cc_final: 0.6763 (p) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.1484 time to fit residues: 7.0455 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.0010 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 1 optimal weight: 0.2980 chunk 0 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.157560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.146828 restraints weight = 2314.890| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.26 r_work: 0.3532 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2034 Z= 0.169 Angle : 0.492 4.494 2760 Z= 0.261 Chirality : 0.043 0.128 304 Planarity : 0.004 0.050 355 Dihedral : 4.026 17.889 334 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 6.37 % Favored : 91.67 % 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: 0.89 (0.55), residues: 244 helix: 0.85 (0.65), residues: 73 sheet: 0.46 (0.78), residues: 48 loop : 0.68 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.002 HIS A 21 PHE 0.006 0.001 PHE B 456 TYR 0.019 0.001 TYR B 495 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.241 Fit side-chains REVERT: A 29 SER cc_start: 0.8228 (t) cc_final: 0.7849 (p) REVERT: B 361 CYS cc_start: 0.7590 (p) cc_final: 0.7006 (p) REVERT: B 380 TYR cc_start: 0.8458 (m-80) cc_final: 0.8230 (m-80) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1381 time to fit residues: 7.1755 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 14 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.0170 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 0.1034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145368 restraints weight = 2312.856| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.12 r_work: 0.3545 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2034 Z= 0.151 Angle : 0.461 3.612 2760 Z= 0.245 Chirality : 0.042 0.124 304 Planarity : 0.004 0.049 355 Dihedral : 3.929 19.348 334 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 8.82 % Favored : 90.20 % 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: 0.87 (0.55), residues: 244 helix: 1.03 (0.64), residues: 73 sheet: 0.06 (0.75), residues: 50 loop : 0.73 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 PHE 0.006 0.001 PHE B 456 TYR 0.018 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.232 Fit side-chains REVERT: A 29 SER cc_start: 0.8255 (t) cc_final: 0.7726 (p) REVERT: B 361 CYS cc_start: 0.7493 (p) cc_final: 0.6898 (p) REVERT: B 380 TYR cc_start: 0.8495 (m-80) cc_final: 0.8290 (m-80) REVERT: B 467 ASP cc_start: 0.7368 (t0) cc_final: 0.6988 (t0) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1435 time to fit residues: 6.9678 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.157326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145870 restraints weight = 2342.952| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 0.94 r_work: 0.3559 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2034 Z= 0.197 Angle : 0.492 6.694 2760 Z= 0.253 Chirality : 0.043 0.124 304 Planarity : 0.004 0.051 355 Dihedral : 3.971 19.710 334 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 8.82 % Favored : 89.71 % 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: 0.93 (0.56), residues: 244 helix: 1.29 (0.65), residues: 73 sheet: 0.05 (0.77), residues: 50 loop : 0.64 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.007 0.001 PHE B 456 TYR 0.018 0.001 TYR B 495 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.222 Fit side-chains REVERT: A 29 SER cc_start: 0.8367 (t) cc_final: 0.7878 (p) REVERT: B 361 CYS cc_start: 0.7469 (p) cc_final: 0.6845 (p) REVERT: B 467 ASP cc_start: 0.7289 (t0) cc_final: 0.6881 (t0) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.1451 time to fit residues: 6.8597 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.1980 chunk 15 optimal weight: 0.0570 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.0170 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150849 restraints weight = 2287.442| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.65 r_work: 0.3605 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2034 Z= 0.162 Angle : 0.473 6.491 2760 Z= 0.243 Chirality : 0.043 0.124 304 Planarity : 0.004 0.049 355 Dihedral : 4.008 22.593 334 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 9.80 % Favored : 88.24 % 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: 0.84 (0.56), residues: 244 helix: 1.30 (0.65), residues: 73 sheet: -0.03 (0.77), residues: 50 loop : 0.53 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 PHE 0.005 0.001 PHE B 456 TYR 0.015 0.001 TYR B 495 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.232 Fit side-chains REVERT: A 29 SER cc_start: 0.8285 (t) cc_final: 0.7742 (p) REVERT: B 361 CYS cc_start: 0.7762 (p) cc_final: 0.7125 (p) REVERT: B 467 ASP cc_start: 0.7546 (t0) cc_final: 0.7177 (t0) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.1427 time to fit residues: 6.6295 Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.0070 chunk 13 optimal weight: 0.0670 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 overall best weight: 0.0690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152122 restraints weight = 2297.961| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.66 r_work: 0.3620 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2034 Z= 0.120 Angle : 0.447 7.785 2760 Z= 0.227 Chirality : 0.042 0.122 304 Planarity : 0.004 0.049 355 Dihedral : 3.916 25.044 334 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.47 % Allowed : 10.29 % Favored : 88.24 % 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: 1.16 (0.55), residues: 244 helix: 1.90 (0.68), residues: 67 sheet: 0.29 (0.87), residues: 39 loop : 0.47 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.003 0.001 PHE B 456 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.224 Fit side-chains REVERT: A 29 SER cc_start: 0.8208 (t) cc_final: 0.7715 (p) REVERT: B 361 CYS cc_start: 0.7683 (p) cc_final: 0.7056 (p) REVERT: B 467 ASP cc_start: 0.7410 (t0) cc_final: 0.7063 (t0) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.1319 time to fit residues: 6.7041 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 0.0980 chunk 4 optimal weight: 0.2980 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 chunk 0 optimal weight: 0.7980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148619 restraints weight = 2357.337| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.67 r_work: 0.3578 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2034 Z= 0.161 Angle : 0.471 8.220 2760 Z= 0.239 Chirality : 0.042 0.121 304 Planarity : 0.004 0.051 355 Dihedral : 3.909 23.754 334 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.47 % Allowed : 10.78 % Favored : 87.75 % 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: 1.08 (0.55), residues: 244 helix: 1.91 (0.69), residues: 67 sheet: 0.25 (0.87), residues: 39 loop : 0.37 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.006 0.001 PHE B 456 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.222 Fit side-chains REVERT: A 17 ASP cc_start: 0.6987 (m-30) cc_final: 0.6472 (m-30) REVERT: A 29 SER cc_start: 0.8249 (t) cc_final: 0.7774 (p) REVERT: B 361 CYS cc_start: 0.7691 (p) cc_final: 0.7081 (p) REVERT: B 457 ARG cc_start: 0.8658 (ttt90) cc_final: 0.8403 (ttt90) REVERT: B 467 ASP cc_start: 0.7420 (t0) cc_final: 0.7076 (t0) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.1352 time to fit residues: 6.5580 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.1980 chunk 20 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 chunk 14 optimal weight: 0.0670 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 0.0570 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 overall best weight: 0.0732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145915 restraints weight = 2426.898| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.66 r_work: 0.3617 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2034 Z= 0.121 Angle : 0.449 8.068 2760 Z= 0.226 Chirality : 0.042 0.127 304 Planarity : 0.004 0.051 355 Dihedral : 3.868 25.589 334 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.98 % Allowed : 11.76 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.55), residues: 244 helix: 1.95 (0.69), residues: 67 sheet: 0.24 (0.87), residues: 39 loop : 0.36 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.003 0.001 PHE B 456 TYR 0.012 0.001 TYR B 495 ARG 0.001 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.224 Fit side-chains REVERT: A 17 ASP cc_start: 0.6962 (m-30) cc_final: 0.6455 (m-30) REVERT: A 29 SER cc_start: 0.8189 (t) cc_final: 0.7727 (p) REVERT: A 38 LYS cc_start: 0.5887 (mmmt) cc_final: 0.4581 (tptp) REVERT: B 361 CYS cc_start: 0.7667 (p) cc_final: 0.7049 (p) REVERT: B 423 TYR cc_start: 0.8817 (t80) cc_final: 0.8418 (t80) REVERT: B 467 ASP cc_start: 0.7384 (t0) cc_final: 0.7033 (t0) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1177 time to fit residues: 5.9060 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0870 chunk 15 optimal weight: 0.0570 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.0170 chunk 2 optimal weight: 0.0970 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.0030 chunk 6 optimal weight: 0.0770 overall best weight: 0.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152665 restraints weight = 2298.236| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.67 r_work: 0.3621 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2034 Z= 0.132 Angle : 0.479 8.441 2760 Z= 0.241 Chirality : 0.042 0.119 304 Planarity : 0.004 0.053 355 Dihedral : 4.115 25.973 334 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.47 % Allowed : 11.76 % Favored : 86.76 % 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 (0.56), residues: 244 helix: 1.96 (0.69), residues: 67 sheet: 0.20 (0.87), residues: 39 loop : 0.36 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.005 0.001 PHE B 392 TYR 0.012 0.001 TYR B 495 ARG 0.001 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.213 Fit side-chains REVERT: A 17 ASP cc_start: 0.6938 (m-30) cc_final: 0.6440 (m-30) REVERT: A 29 SER cc_start: 0.8138 (t) cc_final: 0.7685 (p) REVERT: A 38 LYS cc_start: 0.5831 (mmmt) cc_final: 0.4548 (tptp) REVERT: B 361 CYS cc_start: 0.7666 (p) cc_final: 0.7047 (p) REVERT: B 423 TYR cc_start: 0.8800 (t80) cc_final: 0.8407 (t80) REVERT: B 467 ASP cc_start: 0.7338 (t0) cc_final: 0.6994 (t0) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.1225 time to fit residues: 5.6280 Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142233 restraints weight = 2350.045| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.69 r_work: 0.3553 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2034 Z= 0.278 Angle : 0.565 8.715 2760 Z= 0.284 Chirality : 0.045 0.129 304 Planarity : 0.004 0.050 355 Dihedral : 4.410 22.595 334 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 11.27 % Favored : 86.76 % 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: 0.93 (0.56), residues: 244 helix: 1.92 (0.68), residues: 67 sheet: 0.24 (0.86), residues: 39 loop : 0.16 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.001 0.000 HIS A 21 PHE 0.009 0.001 PHE B 456 TYR 0.022 0.002 TYR B 495 ARG 0.003 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.03 seconds wall clock time: 34 minutes 8.66 seconds (2048.66 seconds total)