Starting phenix.real_space_refine on Wed Jun 4 14:47:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tly_25990/06_2025/7tly_25990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tly_25990/06_2025/7tly_25990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tly_25990/06_2025/7tly_25990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tly_25990/06_2025/7tly_25990.map" model { file = "/net/cci-nas-00/data/ceres_data/7tly_25990/06_2025/7tly_25990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tly_25990/06_2025/7tly_25990.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1990 2.51 5 N 534 2.21 5 O 568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 718 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1388 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.07, per 1000 atoms: 1.63 Number of scatterers: 3105 At special positions: 0 Unit cell: (69.969, 74.184, 79.242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 568 8.00 N 534 7.00 C 1990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.04 Simple disulfide: pdb=" SG CYS I 391 " - pdb=" SG CYS I 525 " distance=2.10 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 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN I 343 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 395.6 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 13.5% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'I' and resid 338 through 343 Processing helix chain 'I' and resid 349 through 353 removed outlier: 3.747A pdb=" N TRP I 353 " --> pdb=" O VAL I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 371 Processing helix chain 'I' and resid 386 through 389 Processing helix chain 'I' and resid 405 through 410 removed outlier: 4.432A pdb=" N ARG I 408 " --> pdb=" O ASP I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 443 Processing helix chain 'I' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.857A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.735A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.040A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'I' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 361 through 362 removed outlier: 6.503A pdb=" N CYS I 361 " --> pdb=" O CYS I 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 452 through 454 126 hydrogen bonds defined for protein. 282 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: 0.93 Time building geometry restraints manager: 1.13 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: 709 1.33 - 1.45: 786 1.45 - 1.58: 1672 1.58 - 1.70: 2 1.70 - 1.83: 16 Bond restraints: 3185 Sorted by residual: bond pdb=" N ASN I 388 " pdb=" CA ASN I 388 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" CB ILE I 332 " pdb=" CG1 ILE I 332 " ideal model delta sigma weight residual 1.530 1.588 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" N ASN I 417 " pdb=" CA ASN I 417 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.35e-02 5.49e+03 7.56e+00 bond pdb=" N PRO B 8 " pdb=" CD PRO B 8 " ideal model delta sigma weight residual 1.474 1.512 -0.038 1.40e-02 5.10e+03 7.56e+00 bond pdb=" NE ARG I 457 " pdb=" CZ ARG I 457 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.55e+00 ... (remaining 3180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 4056 2.31 - 4.62: 217 4.62 - 6.93: 52 6.93 - 9.24: 7 9.24 - 11.55: 4 Bond angle restraints: 4336 Sorted by residual: angle pdb=" N ASP I 389 " pdb=" CA ASP I 389 " pdb=" C ASP I 389 " ideal model delta sigma weight residual 112.92 123.82 -10.90 1.23e+00 6.61e-01 7.85e+01 angle pdb=" N ASP I 389 " pdb=" CA ASP I 389 " pdb=" CB ASP I 389 " ideal model delta sigma weight residual 110.56 99.78 10.78 1.46e+00 4.69e-01 5.45e+01 angle pdb=" C ILE B 59 " pdb=" N PRO B 60 " pdb=" CA PRO B 60 " ideal model delta sigma weight residual 119.78 127.10 -7.32 1.03e+00 9.43e-01 5.06e+01 angle pdb=" C ARG I 498 " pdb=" N PRO I 499 " pdb=" CA PRO I 499 " ideal model delta sigma weight residual 119.87 127.21 -7.34 1.04e+00 9.25e-01 4.98e+01 angle pdb=" C PHE I 490 " pdb=" N PRO I 491 " pdb=" CA PRO I 491 " ideal model delta sigma weight residual 119.56 126.56 -7.00 1.02e+00 9.61e-01 4.71e+01 ... (remaining 4331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 1824 21.31 - 42.61: 52 42.61 - 63.92: 8 63.92 - 85.22: 8 85.22 - 106.53: 5 Dihedral angle restraints: 1897 sinusoidal: 724 harmonic: 1173 Sorted by residual: dihedral pdb=" C ALA B 52 " pdb=" N ALA B 52 " pdb=" CA ALA B 52 " pdb=" CB ALA B 52 " ideal model delta harmonic sigma weight residual -122.60 -136.01 13.41 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" N SER B 53 " pdb=" C SER B 53 " pdb=" CA SER B 53 " pdb=" CB SER B 53 " ideal model delta harmonic sigma weight residual 122.80 112.34 10.46 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.32 32.68 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 1894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 383 0.096 - 0.192: 80 0.192 - 0.288: 12 0.288 - 0.384: 3 0.384 - 0.480: 1 Chirality restraints: 479 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 -2.50 0.10 2.00e-02 2.50e+03 2.53e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.06e+01 chirality pdb=" CA ALA B 52 " pdb=" N ALA B 52 " pdb=" C ALA B 52 " pdb=" CB ALA B 52 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 476 not shown) Planarity restraints: 554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 461 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C LEU I 461 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU I 461 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 462 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 31 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C SER B 31 " 0.031 2.00e-02 2.50e+03 pdb=" O SER B 31 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 32 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 495 " -0.023 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR I 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR I 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR I 495 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 495 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR I 495 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 495 " -0.017 2.00e-02 2.50e+03 ... (remaining 551 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 1742 3.02 - 3.49: 2674 3.49 - 3.96: 5157 3.96 - 4.43: 5922 4.43 - 4.90: 9437 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" O GLN B 6 " pdb=" OG SER B 7 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP A 115 " pdb=" N ASN A 116 " model vdw 2.586 3.120 nonbonded pdb=" N ASP I 428 " pdb=" OD1 ASP I 428 " model vdw 2.591 3.120 nonbonded pdb=" N LEU I 387 " pdb=" N ASN I 388 " model vdw 2.592 2.560 nonbonded pdb=" N LYS I 462 " pdb=" O LYS I 462 " model vdw 2.611 2.496 ... (remaining 24927 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: 9.040 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.030 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.010 0.074 3194 Z= 0.576 Angle : 1.328 11.553 4358 Z= 0.895 Chirality : 0.083 0.480 479 Planarity : 0.005 0.025 553 Dihedral : 12.976 106.526 1138 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.41), residues: 396 helix: -3.25 (0.69), residues: 33 sheet: 0.71 (0.40), residues: 157 loop : 0.65 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.013 0.003 PHE B 98 TYR 0.023 0.003 TYR I 495 ARG 0.003 0.000 ARG I 493 Details of bonding type rmsd link_NAG-ASN : bond 0.05745 ( 1) link_NAG-ASN : angle 2.44605 ( 3) link_BETA1-4 : bond 0.05749 ( 2) link_BETA1-4 : angle 2.55125 ( 6) hydrogen bonds : bond 0.17018 ( 116) hydrogen bonds : angle 8.84395 ( 282) link_BETA1-6 : bond 0.04853 ( 1) link_BETA1-6 : angle 1.46037 ( 3) SS BOND : bond 0.03371 ( 5) SS BOND : angle 2.51708 ( 10) covalent geometry : bond 0.00998 ( 3185) covalent geometry : angle 1.32024 ( 4336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.5815 (m-30) cc_final: 0.5444 (m-30) REVERT: A 95 TYR cc_start: 0.7806 (m-80) cc_final: 0.7444 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 1.1649 time to fit residues: 76.7483 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.165589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.154344 restraints weight = 4083.401| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.37 r_work: 0.3586 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3194 Z= 0.158 Angle : 0.631 9.699 4358 Z= 0.316 Chirality : 0.049 0.162 479 Planarity : 0.005 0.052 553 Dihedral : 7.520 51.280 531 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.16 % Allowed : 9.12 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.01 (0.40), residues: 396 helix: -2.53 (0.99), residues: 26 sheet: 0.66 (0.40), residues: 152 loop : -0.08 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 436 HIS 0.002 0.002 HIS I 505 PHE 0.014 0.002 PHE I 429 TYR 0.015 0.002 TYR A 94 ARG 0.006 0.001 ARG I 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 1) link_NAG-ASN : angle 1.72819 ( 3) link_BETA1-4 : bond 0.00516 ( 2) link_BETA1-4 : angle 2.53564 ( 6) hydrogen bonds : bond 0.03907 ( 116) hydrogen bonds : angle 6.53962 ( 282) link_BETA1-6 : bond 0.00116 ( 1) link_BETA1-6 : angle 1.52609 ( 3) SS BOND : bond 0.00227 ( 5) SS BOND : angle 1.02792 ( 10) covalent geometry : bond 0.00353 ( 3185) covalent geometry : angle 0.62066 ( 4336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7099 (mm-40) REVERT: B 43 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7814 (mt0) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 1.2267 time to fit residues: 69.4464 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.158323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.148640 restraints weight = 4050.526| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.12 r_work: 0.3514 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 3194 Z= 0.281 Angle : 0.750 11.178 4358 Z= 0.377 Chirality : 0.052 0.159 479 Planarity : 0.006 0.057 553 Dihedral : 5.920 37.502 531 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.46 % Allowed : 12.28 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.39), residues: 396 helix: -3.16 (0.77), residues: 32 sheet: 0.30 (0.41), residues: 141 loop : -0.66 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 50 HIS 0.004 0.002 HIS B 92 PHE 0.018 0.002 PHE I 429 TYR 0.021 0.002 TYR A 95 ARG 0.004 0.001 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 1) link_NAG-ASN : angle 1.13718 ( 3) link_BETA1-4 : bond 0.00490 ( 2) link_BETA1-4 : angle 2.29921 ( 6) hydrogen bonds : bond 0.05372 ( 116) hydrogen bonds : angle 6.61339 ( 282) link_BETA1-6 : bond 0.00082 ( 1) link_BETA1-6 : angle 1.68486 ( 3) SS BOND : bond 0.00385 ( 5) SS BOND : angle 1.39646 ( 10) covalent geometry : bond 0.00660 ( 3185) covalent geometry : angle 0.74185 ( 4336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.329 Fit side-chains REVERT: A 59 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7968 (t0) REVERT: I 457 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7817 (ttt90) outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 1.3066 time to fit residues: 59.2117 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.0060 chunk 6 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.161188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.151574 restraints weight = 4113.415| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.14 r_work: 0.3553 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3194 Z= 0.118 Angle : 0.535 9.154 4358 Z= 0.270 Chirality : 0.044 0.147 479 Planarity : 0.005 0.052 553 Dihedral : 4.651 26.872 531 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.81 % Allowed : 11.58 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.63 (0.40), residues: 396 helix: -2.84 (0.90), residues: 26 sheet: 0.52 (0.42), residues: 140 loop : -0.71 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.006 0.001 PHE I 374 TYR 0.016 0.001 TYR A 95 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 1) link_NAG-ASN : angle 1.45874 ( 3) link_BETA1-4 : bond 0.00503 ( 2) link_BETA1-4 : angle 2.19420 ( 6) hydrogen bonds : bond 0.03689 ( 116) hydrogen bonds : angle 6.09692 ( 282) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.31254 ( 3) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.80577 ( 10) covalent geometry : bond 0.00261 ( 3185) covalent geometry : angle 0.52631 ( 4336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.376 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 1.2567 time to fit residues: 63.4129 Evaluate side-chains 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.156902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.147322 restraints weight = 4090.904| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.12 r_work: 0.3503 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3194 Z= 0.273 Angle : 0.702 12.276 4358 Z= 0.352 Chirality : 0.050 0.156 479 Planarity : 0.006 0.060 553 Dihedral : 5.082 19.266 531 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.21 % Allowed : 12.63 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.21 (0.39), residues: 396 helix: -3.30 (0.74), residues: 33 sheet: 0.19 (0.42), residues: 143 loop : -1.06 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 50 HIS 0.003 0.002 HIS B 92 PHE 0.012 0.002 PHE I 429 TYR 0.020 0.002 TYR A 95 ARG 0.004 0.001 ARG I 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 1) link_NAG-ASN : angle 1.11326 ( 3) link_BETA1-4 : bond 0.00502 ( 2) link_BETA1-4 : angle 2.01324 ( 6) hydrogen bonds : bond 0.04966 ( 116) hydrogen bonds : angle 6.48456 ( 282) link_BETA1-6 : bond 0.00141 ( 1) link_BETA1-6 : angle 1.62418 ( 3) SS BOND : bond 0.00357 ( 5) SS BOND : angle 1.27883 ( 10) covalent geometry : bond 0.00641 ( 3185) covalent geometry : angle 0.69468 ( 4336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.360 Fit side-chains REVERT: A 119 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: I 465 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (tt0) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 1.1958 time to fit residues: 57.8894 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 465 GLU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.158186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.148679 restraints weight = 4197.757| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.13 r_work: 0.3511 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3194 Z= 0.195 Angle : 0.615 11.618 4358 Z= 0.307 Chirality : 0.046 0.140 479 Planarity : 0.006 0.054 553 Dihedral : 4.630 18.555 531 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.56 % Allowed : 12.28 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.29 (0.39), residues: 396 helix: -3.38 (0.71), residues: 33 sheet: 0.20 (0.42), residues: 143 loop : -1.16 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 PHE 0.009 0.001 PHE B 63 TYR 0.019 0.002 TYR A 95 ARG 0.003 0.001 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 1) link_NAG-ASN : angle 1.22988 ( 3) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 1.98761 ( 6) hydrogen bonds : bond 0.04267 ( 116) hydrogen bonds : angle 6.31358 ( 282) link_BETA1-6 : bond 0.00005 ( 1) link_BETA1-6 : angle 1.46107 ( 3) SS BOND : bond 0.00333 ( 5) SS BOND : angle 1.04382 ( 10) covalent geometry : bond 0.00458 ( 3185) covalent geometry : angle 0.60789 ( 4336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.384 Fit side-chains REVERT: A 119 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: I 441 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7729 (tt) REVERT: I 465 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7713 (tt0) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 1.2876 time to fit residues: 62.2662 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 465 GLU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.0000 chunk 14 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 overall best weight: 0.3582 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.159116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.149752 restraints weight = 4100.845| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.11 r_work: 0.3526 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3194 Z= 0.155 Angle : 0.564 10.102 4358 Z= 0.284 Chirality : 0.045 0.138 479 Planarity : 0.006 0.053 553 Dihedral : 4.357 18.303 531 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.86 % Allowed : 13.33 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.18 (0.39), residues: 396 helix: -3.40 (0.71), residues: 33 sheet: 0.31 (0.43), residues: 142 loop : -1.10 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 117 HIS 0.002 0.001 HIS B 92 PHE 0.011 0.001 PHE I 392 TYR 0.018 0.001 TYR A 95 ARG 0.005 0.001 ARG I 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 1.23787 ( 3) link_BETA1-4 : bond 0.00459 ( 2) link_BETA1-4 : angle 1.84661 ( 6) hydrogen bonds : bond 0.03914 ( 116) hydrogen bonds : angle 6.17193 ( 282) link_BETA1-6 : bond 0.00053 ( 1) link_BETA1-6 : angle 1.41723 ( 3) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.87822 ( 10) covalent geometry : bond 0.00360 ( 3185) covalent geometry : angle 0.55765 ( 4336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.353 Fit side-chains REVERT: A 119 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.6755 (pm20) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 1.2266 time to fit residues: 54.3898 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.157933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.148227 restraints weight = 4091.124| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.14 r_work: 0.3498 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3194 Z= 0.217 Angle : 0.637 11.343 4358 Z= 0.319 Chirality : 0.047 0.147 479 Planarity : 0.006 0.054 553 Dihedral : 4.652 19.117 531 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.21 % Allowed : 12.98 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.40 (0.39), residues: 396 helix: -3.40 (0.71), residues: 33 sheet: 0.15 (0.43), residues: 143 loop : -1.27 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 117 HIS 0.003 0.001 HIS B 92 PHE 0.010 0.002 PHE I 392 TYR 0.019 0.002 TYR A 95 ARG 0.008 0.001 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 1) link_NAG-ASN : angle 1.13861 ( 3) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 1.81549 ( 6) hydrogen bonds : bond 0.04362 ( 116) hydrogen bonds : angle 6.38323 ( 282) link_BETA1-6 : bond 0.00049 ( 1) link_BETA1-6 : angle 1.54252 ( 3) SS BOND : bond 0.00347 ( 5) SS BOND : angle 1.06311 ( 10) covalent geometry : bond 0.00512 ( 3185) covalent geometry : angle 0.63138 ( 4336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.392 Fit side-chains REVERT: A 119 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6718 (pm20) outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 1.2262 time to fit residues: 56.9054 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.148922 restraints weight = 4099.294| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.10 r_work: 0.3513 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3194 Z= 0.184 Angle : 0.605 10.878 4358 Z= 0.303 Chirality : 0.046 0.142 479 Planarity : 0.006 0.056 553 Dihedral : 4.506 18.774 531 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.51 % Allowed : 14.74 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.41 (0.39), residues: 396 helix: -3.42 (0.70), residues: 33 sheet: 0.13 (0.43), residues: 144 loop : -1.27 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 117 HIS 0.003 0.001 HIS B 92 PHE 0.008 0.001 PHE I 392 TYR 0.018 0.001 TYR A 95 ARG 0.010 0.001 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 1.19923 ( 3) link_BETA1-4 : bond 0.00371 ( 2) link_BETA1-4 : angle 1.78144 ( 6) hydrogen bonds : bond 0.04046 ( 116) hydrogen bonds : angle 6.29715 ( 282) link_BETA1-6 : bond 0.00067 ( 1) link_BETA1-6 : angle 1.39148 ( 3) SS BOND : bond 0.00309 ( 5) SS BOND : angle 0.95797 ( 10) covalent geometry : bond 0.00436 ( 3185) covalent geometry : angle 0.59900 ( 4336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.328 Fit side-chains REVERT: A 90 ASP cc_start: 0.6832 (m-30) cc_final: 0.6222 (m-30) REVERT: A 119 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: B 24 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7752 (tpp80) outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 1.3511 time to fit residues: 61.3778 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 34 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.158607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.149405 restraints weight = 4064.264| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.08 r_work: 0.3520 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3194 Z= 0.163 Angle : 0.584 10.096 4358 Z= 0.294 Chirality : 0.045 0.140 479 Planarity : 0.006 0.055 553 Dihedral : 4.433 18.448 531 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.16 % Allowed : 16.14 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.40 (0.39), residues: 396 helix: -3.46 (0.68), residues: 33 sheet: 0.14 (0.43), residues: 144 loop : -1.26 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 117 HIS 0.002 0.001 HIS B 92 PHE 0.007 0.001 PHE I 392 TYR 0.018 0.001 TYR A 95 ARG 0.011 0.001 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 1) link_NAG-ASN : angle 1.17228 ( 3) link_BETA1-4 : bond 0.00373 ( 2) link_BETA1-4 : angle 1.71552 ( 6) hydrogen bonds : bond 0.03868 ( 116) hydrogen bonds : angle 6.21912 ( 282) link_BETA1-6 : bond 0.00054 ( 1) link_BETA1-6 : angle 1.42503 ( 3) SS BOND : bond 0.00292 ( 5) SS BOND : angle 0.90678 ( 10) covalent geometry : bond 0.00382 ( 3185) covalent geometry : angle 0.57855 ( 4336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.365 Fit side-chains REVERT: A 90 ASP cc_start: 0.6803 (m-30) cc_final: 0.6189 (m-30) REVERT: A 119 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: B 24 ARG cc_start: 0.7980 (tpp80) cc_final: 0.7728 (tpp80) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 1.3034 time to fit residues: 57.7252 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.0000 chunk 30 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.0718 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.153207 restraints weight = 4091.300| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.10 r_work: 0.3571 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3194 Z= 0.083 Angle : 0.479 5.517 4358 Z= 0.245 Chirality : 0.043 0.132 479 Planarity : 0.005 0.053 553 Dihedral : 3.950 17.981 531 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.81 % Allowed : 15.79 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.39), residues: 396 helix: -3.39 (0.70), residues: 32 sheet: 0.44 (0.44), residues: 141 loop : -1.08 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 436 HIS 0.001 0.000 HIS B 92 PHE 0.006 0.001 PHE I 400 TYR 0.016 0.001 TYR A 95 ARG 0.009 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 1.39394 ( 3) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 1.57056 ( 6) hydrogen bonds : bond 0.02944 ( 116) hydrogen bonds : angle 5.73900 ( 282) link_BETA1-6 : bond 0.00318 ( 1) link_BETA1-6 : angle 1.20858 ( 3) SS BOND : bond 0.00199 ( 5) SS BOND : angle 0.62769 ( 10) covalent geometry : bond 0.00181 ( 3185) covalent geometry : angle 0.47334 ( 4336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.67 seconds wall clock time: 53 minutes 31.90 seconds (3211.90 seconds total)