Starting phenix.real_space_refine on Wed Jul 23 07:34:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzu_22574/07_2025/7jzu_22574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzu_22574/07_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_22574/07_2025/7jzu_22574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzu_22574/07_2025/7jzu_22574.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzu_22574/07_2025/7jzu_22574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzu_22574/07_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-5711/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: 3.29, per 1000 atoms: 1.66 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: 0.68 Conformation dependent library (CDL) restraints added in 246.9 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: 0.48 Time building geometry restraints manager: 0.73 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.170 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:2.850 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- 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 0.126 2041 Z= 0.818 Angle : 1.357 7.124 2777 Z= 0.905 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 Details of bonding type rmsd link_NAG-ASN : bond 0.05641 ( 1) link_NAG-ASN : angle 2.67644 ( 3) link_BETA1-4 : bond 0.07263 ( 1) link_BETA1-4 : angle 3.79002 ( 3) hydrogen bonds : bond 0.18316 ( 80) hydrogen bonds : angle 8.72729 ( 204) link_BETA1-6 : bond 0.05027 ( 1) link_BETA1-6 : angle 2.19551 ( 3) SS BOND : bond 0.07104 ( 4) SS BOND : angle 2.48932 ( 8) covalent geometry : bond 0.01477 ( 2034) covalent geometry : angle 1.34354 ( 2760) *********************** 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 : 0.268 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: 0.1719 time to fit residues: 9.6420 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 : 0.227 ------------------------------------------------------------------------------- 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 = 0.157601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144589 restraints weight = 2305.124| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.13 r_work: 0.3495 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 2041 Z= 0.182 Angle : 0.616 7.138 2777 Z= 0.316 Chirality : 0.045 0.165 304 Planarity : 0.004 0.041 355 Dihedral : 4.365 15.504 334 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 2.12432 ( 3) link_BETA1-4 : bond 0.00001 ( 1) link_BETA1-4 : angle 2.26512 ( 3) hydrogen bonds : bond 0.05187 ( 80) hydrogen bonds : angle 6.34626 ( 204) link_BETA1-6 : bond 0.00042 ( 1) link_BETA1-6 : angle 1.66147 ( 3) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.53472 ( 8) covalent geometry : bond 0.00417 ( 2034) covalent geometry : angle 0.60591 ( 2760) *********************** 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 : 0.231 Fit side-chains REVERT: A 13 MET cc_start: 0.8468 (ptm) cc_final: 0.8055 (ptt) REVERT: A 29 SER cc_start: 0.8273 (t) cc_final: 0.7814 (p) REVERT: B 361 CYS cc_start: 0.7393 (p) cc_final: 0.6758 (p) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.1440 time to fit residues: 6.8019 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 : 0.228 ------------------------------------------------------------------------------- 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: 0.1980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 0 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 17 optimal weight: 0.2980 overall best weight: 0.1780 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144431 restraints weight = 2319.563| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.26 r_work: 0.3485 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2041 Z= 0.144 Angle : 0.527 4.953 2777 Z= 0.275 Chirality : 0.043 0.133 304 Planarity : 0.004 0.050 355 Dihedral : 4.139 17.475 334 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.96 % Allowed : 6.86 % Favored : 91.18 % 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: 0.83 (0.55), residues: 244 helix: 0.83 (0.65), residues: 73 sheet: 0.42 (0.77), residues: 48 loop : 0.62 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.002 HIS A 21 PHE 0.007 0.001 PHE B 456 TYR 0.021 0.002 TYR B 495 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.87497 ( 3) link_BETA1-4 : bond 0.00428 ( 1) link_BETA1-4 : angle 1.95447 ( 3) hydrogen bonds : bond 0.04321 ( 80) hydrogen bonds : angle 5.79282 ( 204) link_BETA1-6 : bond 0.00083 ( 1) link_BETA1-6 : angle 1.33516 ( 3) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.44218 ( 8) covalent geometry : bond 0.00325 ( 2034) covalent geometry : angle 0.51815 ( 2760) *********************** 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 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.231 Fit side-chains REVERT: A 29 SER cc_start: 0.8262 (t) cc_final: 0.7874 (p) REVERT: B 361 CYS cc_start: 0.7674 (p) cc_final: 0.7048 (p) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.1661 time to fit residues: 7.4973 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.0980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 14 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 22 optimal weight: 0.0870 chunk 13 optimal weight: 0.0970 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 9 optimal weight: 0.0470 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 = 0.3740 r_free = 0.3740 target = 0.157582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144925 restraints weight = 2307.066| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.12 r_work: 0.3523 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2041 Z= 0.098 Angle : 0.471 3.562 2777 Z= 0.246 Chirality : 0.042 0.124 304 Planarity : 0.004 0.049 355 Dihedral : 3.985 20.706 334 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.44 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: 0.88 (0.56), residues: 244 helix: 1.10 (0.65), residues: 73 sheet: 0.07 (0.75), residues: 50 loop : 0.69 (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 0.016 0.001 TYR B 495 ARG 0.005 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 1) link_NAG-ASN : angle 1.51061 ( 3) link_BETA1-4 : bond 0.00288 ( 1) link_BETA1-4 : angle 1.68389 ( 3) hydrogen bonds : bond 0.03664 ( 80) hydrogen bonds : angle 5.51374 ( 204) link_BETA1-6 : bond 0.00211 ( 1) link_BETA1-6 : angle 1.31192 ( 3) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.81563 ( 8) covalent geometry : bond 0.00209 ( 2034) covalent geometry : angle 0.46202 ( 2760) *********************** 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 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.232 Fit side-chains REVERT: A 29 SER cc_start: 0.8259 (t) cc_final: 0.7721 (p) REVERT: B 361 CYS cc_start: 0.7507 (p) cc_final: 0.6915 (p) outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.1534 time to fit residues: 7.7091 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 : 0.184 ------------------------------------------------------------------------------- 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: 0.0970 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 0.2980 overall best weight: 0.1136 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.161144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150829 restraints weight = 2320.999| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 0.82 r_work: 0.3618 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2041 Z= 0.106 Angle : 0.480 7.143 2777 Z= 0.245 Chirality : 0.042 0.123 304 Planarity : 0.004 0.050 355 Dihedral : 3.929 21.386 334 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.45 % Allowed : 8.33 % Favored : 89.22 % 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: 1.22 (0.65), residues: 73 sheet: 0.09 (0.78), residues: 50 loop : 0.66 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 PHE 0.005 0.001 PHE B 456 TYR 0.017 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 1.67082 ( 3) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 1.81474 ( 3) hydrogen bonds : bond 0.03384 ( 80) hydrogen bonds : angle 5.46186 ( 204) link_BETA1-6 : bond 0.00181 ( 1) link_BETA1-6 : angle 1.28882 ( 3) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.93733 ( 8) covalent geometry : bond 0.00233 ( 2034) covalent geometry : angle 0.47030 ( 2760) *********************** 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 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.232 Fit side-chains REVERT: A 29 SER cc_start: 0.8298 (t) cc_final: 0.7835 (p) REVERT: B 361 CYS cc_start: 0.7190 (p) cc_final: 0.6585 (p) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.1433 time to fit residues: 6.7906 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASP 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: 0.4980 chunk 15 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 7 optimal weight: 0.2980 chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 0.1980 chunk 0 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 overall best weight: 0.1536 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.164532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148389 restraints weight = 2298.381| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.61 r_work: 0.3612 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2041 Z= 0.123 Angle : 0.501 6.883 2777 Z= 0.251 Chirality : 0.042 0.123 304 Planarity : 0.004 0.050 355 Dihedral : 4.014 21.947 334 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.67 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: 0.98 (0.56), residues: 244 helix: 1.42 (0.67), residues: 73 sheet: 0.29 (0.87), residues: 40 loop : 0.47 (0.55), residues: 131 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 0.005 0.001 PHE B 456 TYR 0.016 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 1.88255 ( 3) link_BETA1-4 : bond 0.00235 ( 1) link_BETA1-4 : angle 2.00855 ( 3) hydrogen bonds : bond 0.03524 ( 80) hydrogen bonds : angle 5.51623 ( 204) link_BETA1-6 : bond 0.00115 ( 1) link_BETA1-6 : angle 1.24710 ( 3) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.89030 ( 8) covalent geometry : bond 0.00285 ( 2034) covalent geometry : angle 0.49040 ( 2760) *********************** 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 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.180 Fit side-chains REVERT: A 17 ASP cc_start: 0.7105 (m-30) cc_final: 0.6529 (m-30) REVERT: A 29 SER cc_start: 0.8278 (t) cc_final: 0.7770 (p) REVERT: B 361 CYS cc_start: 0.7740 (p) cc_final: 0.7103 (p) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.1350 time to fit residues: 6.5447 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 : 0.229 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 10 optimal weight: 0.0970 chunk 2 optimal weight: 0.0670 chunk 12 optimal weight: 0.0980 chunk 1 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 overall best weight: 0.1116 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.167969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151779 restraints weight = 2275.187| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.62 r_work: 0.3621 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.002 0.027 2041 Z= 0.099 Angle : 0.466 7.334 2777 Z= 0.234 Chirality : 0.042 0.126 304 Planarity : 0.004 0.051 355 Dihedral : 4.001 25.250 334 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.44 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: 1.23 (0.55), residues: 244 helix: 2.03 (0.69), residues: 67 sheet: 0.32 (0.88), 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 0.004 0.001 PHE B 456 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 1.63871 ( 3) link_BETA1-4 : bond 0.00296 ( 1) link_BETA1-4 : angle 1.77424 ( 3) hydrogen bonds : bond 0.03147 ( 80) hydrogen bonds : angle 5.45017 ( 204) link_BETA1-6 : bond 0.00244 ( 1) link_BETA1-6 : angle 1.21783 ( 3) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.84480 ( 8) covalent geometry : bond 0.00225 ( 2034) covalent geometry : angle 0.45675 ( 2760) *********************** 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 : 0.205 Fit side-chains REVERT: A 17 ASP cc_start: 0.7050 (m-30) cc_final: 0.6507 (m-30) REVERT: A 29 SER cc_start: 0.8230 (t) cc_final: 0.7761 (p) REVERT: A 38 LYS cc_start: 0.6040 (mmmt) cc_final: 0.4698 (tptp) REVERT: B 361 CYS cc_start: 0.7690 (p) cc_final: 0.7075 (p) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.1362 time to fit residues: 6.9284 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 : 0.242 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 22 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 chunk 4 optimal weight: 0.0970 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148866 restraints weight = 2325.375| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.69 r_work: 0.3595 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2041 Z= 0.121 Angle : 0.504 8.138 2777 Z= 0.250 Chirality : 0.043 0.121 304 Planarity : 0.004 0.050 355 Dihedral : 4.061 24.389 334 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 1.10 (0.55), residues: 244 helix: 2.00 (0.69), residues: 67 sheet: 0.34 (0.87), residues: 39 loop : 0.30 (0.53), residues: 138 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 0.006 0.001 PHE B 456 TYR 0.017 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 1) link_NAG-ASN : angle 1.95711 ( 3) link_BETA1-4 : bond 0.00250 ( 1) link_BETA1-4 : angle 2.07418 ( 3) hydrogen bonds : bond 0.03402 ( 80) hydrogen bonds : angle 5.52347 ( 204) link_BETA1-6 : bond 0.00214 ( 1) link_BETA1-6 : angle 1.14384 ( 3) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.15779 ( 8) covalent geometry : bond 0.00282 ( 2034) covalent geometry : angle 0.49092 ( 2760) *********************** 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 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.223 Fit side-chains REVERT: A 17 ASP cc_start: 0.7103 (m-30) cc_final: 0.6578 (m-30) REVERT: A 29 SER cc_start: 0.8241 (t) cc_final: 0.7781 (p) REVERT: A 38 LYS cc_start: 0.6149 (mmmt) cc_final: 0.4791 (tptp) REVERT: B 361 CYS cc_start: 0.7724 (p) cc_final: 0.7091 (p) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.1226 time to fit residues: 5.9725 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 : 0.236 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 14 optimal weight: 0.0060 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 0 optimal weight: 0.7980 overall best weight: 0.0934 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.166862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149940 restraints weight = 2359.034| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.72 r_work: 0.3603 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2041 Z= 0.091 Angle : 0.469 8.283 2777 Z= 0.233 Chirality : 0.042 0.120 304 Planarity : 0.004 0.050 355 Dihedral : 4.053 27.000 334 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 8.82 % Favored : 89.22 % 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: 1.07 (0.55), residues: 244 helix: 2.01 (0.69), residues: 67 sheet: 0.32 (0.87), residues: 39 loop : 0.27 (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 0.004 0.001 PHE B 400 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 1.62196 ( 3) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 1.77891 ( 3) hydrogen bonds : bond 0.03094 ( 80) hydrogen bonds : angle 5.42388 ( 204) link_BETA1-6 : bond 0.00236 ( 1) link_BETA1-6 : angle 1.18462 ( 3) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.96972 ( 8) covalent geometry : bond 0.00203 ( 2034) covalent geometry : angle 0.45897 ( 2760) *********************** 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: 4 poor density : 39 time to evaluate : 0.210 Fit side-chains REVERT: A 17 ASP cc_start: 0.7113 (m-30) cc_final: 0.6569 (m-30) REVERT: A 29 SER cc_start: 0.8190 (t) cc_final: 0.7747 (p) REVERT: A 38 LYS cc_start: 0.6105 (mmmt) cc_final: 0.4714 (tptp) REVERT: B 361 CYS cc_start: 0.7690 (p) cc_final: 0.7069 (p) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.1167 time to fit residues: 5.5214 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0870 chunk 15 optimal weight: 0.0270 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 0.0370 chunk 6 optimal weight: 0.0870 overall best weight: 0.0670 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.164808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148379 restraints weight = 2312.527| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.65 r_work: 0.3577 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: 0.7638 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2041 Z= 0.084 Angle : 0.467 8.270 2777 Z= 0.231 Chirality : 0.041 0.120 304 Planarity : 0.004 0.051 355 Dihedral : 4.012 27.933 334 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.19 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: 1.12 (0.55), residues: 244 helix: 2.07 (0.69), residues: 67 sheet: 0.29 (0.87), residues: 39 loop : 0.32 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 PHE 0.003 0.001 PHE B 456 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00016 ( 1) link_NAG-ASN : angle 1.47400 ( 3) link_BETA1-4 : bond 0.00333 ( 1) link_BETA1-4 : angle 1.64494 ( 3) hydrogen bonds : bond 0.02954 ( 80) hydrogen bonds : angle 5.36909 ( 204) link_BETA1-6 : bond 0.00257 ( 1) link_BETA1-6 : angle 1.19131 ( 3) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.93246 ( 8) covalent geometry : bond 0.00186 ( 2034) covalent geometry : angle 0.45873 ( 2760) ********************** 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 : 0.233 Fit side-chains REVERT: A 13 MET cc_start: 0.8039 (ttp) cc_final: 0.7744 (ttp) REVERT: A 17 ASP cc_start: 0.7113 (m-30) cc_final: 0.6578 (m-30) REVERT: A 38 LYS cc_start: 0.6086 (mmmt) cc_final: 0.4742 (tptp) REVERT: B 361 CYS cc_start: 0.7655 (p) cc_final: 0.7056 (p) REVERT: B 465 GLU cc_start: 0.8424 (tt0) cc_final: 0.8206 (tt0) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.1442 time to fit residues: 6.6388 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 : 0.223 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.0050 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 overall best weight: 0.1148 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.167321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150815 restraints weight = 2311.081| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.67 r_work: 0.3614 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2041 Z= 0.101 Angle : 0.479 8.256 2777 Z= 0.238 Chirality : 0.042 0.119 304 Planarity : 0.004 0.051 355 Dihedral : 4.004 27.091 334 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.45 % Allowed : 8.82 % Favored : 88.73 % 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: 1.11 (0.55), residues: 244 helix: 2.08 (0.69), residues: 67 sheet: 0.27 (0.86), residues: 39 loop : 0.29 (0.53), residues: 138 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 0.004 0.001 PHE B 456 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 1.70629 ( 3) link_BETA1-4 : bond 0.00299 ( 1) link_BETA1-4 : angle 1.76116 ( 3) hydrogen bonds : bond 0.03057 ( 80) hydrogen bonds : angle 5.42512 ( 204) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.14469 ( 3) SS BOND : bond 0.00198 ( 4) SS BOND : angle 1.03035 ( 8) covalent geometry : bond 0.00232 ( 2034) covalent geometry : angle 0.46889 ( 2760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.49 seconds wall clock time: 34 minutes 25.53 seconds (2065.53 seconds total)