Starting phenix.real_space_refine on Wed Jul 23 13:30:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpz_27644/07_2025/8dpz_27644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpz_27644/07_2025/8dpz_27644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2025/8dpz_27644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2025/8dpz_27644.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2025/8dpz_27644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2025/8dpz_27644.cif" } resolution = 3.38 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= -0.017 sd= 0.107 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 2115 2.51 5 N 551 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.85, per 1000 atoms: 1.46 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.28, 90.72, 74.52, 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 649 8.00 N 551 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 506.6 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 11.2% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.210A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.822A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN F 33 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.623A pdb=" N GLN F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.536A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR G 49 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 324 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: 1.29 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 898 1.46 - 1.58: 1458 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 3413 Sorted by residual: bond pdb=" C GLU G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.43e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C SER G 7 " pdb=" N PRO G 8 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" CB ASP F 100A" pdb=" CG ASP F 100A" ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 ... (remaining 3408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4413 1.63 - 3.26: 188 3.26 - 4.89: 31 4.89 - 6.51: 7 6.51 - 8.14: 3 Bond angle restraints: 4642 Sorted by residual: angle pdb=" C ASP G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" N ASP F 100 " pdb=" CA ASP F 100 " pdb=" C ASP F 100 " ideal model delta sigma weight residual 109.95 105.91 4.04 1.44e+00 4.82e-01 7.86e+00 angle pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta sigma weight residual 120.06 123.39 -3.33 1.19e+00 7.06e-01 7.81e+00 angle pdb=" C PHE G 83 " pdb=" CA PHE G 83 " pdb=" CB PHE G 83 " ideal model delta sigma weight residual 111.31 115.81 -4.50 1.68e+00 3.54e-01 7.18e+00 angle pdb=" N TRP G 94 " pdb=" CA TRP G 94 " pdb=" C TRP G 94 " ideal model delta sigma weight residual 113.57 117.12 -3.55 1.38e+00 5.25e-01 6.62e+00 ... (remaining 4637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1822 16.50 - 33.01: 177 33.01 - 49.51: 25 49.51 - 66.02: 5 66.02 - 82.52: 4 Dihedral angle restraints: 2033 sinusoidal: 817 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.65 36.35 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA VAL F 95 " pdb=" C VAL F 95 " pdb=" N ALA F 96 " pdb=" CA ALA F 96 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN G 93 " pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 290 0.035 - 0.070: 137 0.070 - 0.106: 51 0.106 - 0.141: 19 0.141 - 0.176: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB THR G 102 " pdb=" CA THR G 102 " pdb=" OG1 THR G 102 " pdb=" CG2 THR G 102 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA TRP G 94 " pdb=" N TRP G 94 " pdb=" C TRP G 94 " pdb=" CB TRP G 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 498 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 79 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO B 337 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 83 " -0.014 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE G 83 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1186 2.87 - 3.38: 2663 3.38 - 3.89: 5282 3.89 - 4.39: 5920 4.39 - 4.90: 10828 Nonbonded interactions: 25879 Sorted by model distance: nonbonded pdb=" OH TYR F 97 " pdb=" OE1 GLU F 99 " model vdw 2.363 3.040 nonbonded pdb=" OD2 ASP B 405 " pdb=" OG SER G 30 " model vdw 2.408 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.420 3.120 nonbonded pdb=" OD1 ASP F 100 " pdb=" N ASP F 100A" model vdw 2.427 3.120 nonbonded pdb=" NH1 ARG G 61 " pdb=" OD2 ASP G 82 " model vdw 2.429 3.120 ... (remaining 25874 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: 34.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 56.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.042 3420 Z= 0.188 Angle : 0.774 8.142 4658 Z= 0.412 Chirality : 0.050 0.176 501 Planarity : 0.007 0.069 595 Dihedral : 13.012 82.522 1248 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -2.09 (0.38), residues: 412 helix: -4.20 (0.35), residues: 27 sheet: -0.08 (0.45), residues: 139 loop : -1.92 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 103 HIS 0.001 0.001 HIS B 519 PHE 0.037 0.003 PHE G 83 TYR 0.018 0.002 TYR G 49 ARG 0.006 0.001 ARG G 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 2.27697 ( 3) link_BETA1-4 : bond 0.00751 ( 1) link_BETA1-4 : angle 1.33408 ( 3) hydrogen bonds : bond 0.24268 ( 104) hydrogen bonds : angle 10.69454 ( 324) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.64337 ( 10) covalent geometry : bond 0.00416 ( 3413) covalent geometry : angle 0.77180 ( 4642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.445 Fit side-chains REVERT: B 406 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 417 LYS cc_start: 0.8402 (tppt) cc_final: 0.8171 (tptt) REVERT: F 48 ILE cc_start: 0.8306 (mm) cc_final: 0.7982 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2140 time to fit residues: 16.4200 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.117241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097683 restraints weight = 5099.351| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3136 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3420 Z= 0.215 Angle : 0.640 6.446 4658 Z= 0.339 Chirality : 0.046 0.167 501 Planarity : 0.005 0.047 595 Dihedral : 5.320 23.782 510 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.83 % Allowed : 6.11 % Favored : 93.06 % 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: -1.69 (0.39), residues: 412 helix: -3.74 (0.53), residues: 28 sheet: 0.21 (0.47), residues: 140 loop : -1.67 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.024 0.003 PHE G 83 TYR 0.014 0.002 TYR B 453 ARG 0.003 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.66356 ( 3) link_BETA1-4 : bond 0.00529 ( 1) link_BETA1-4 : angle 1.28912 ( 3) hydrogen bonds : bond 0.04720 ( 104) hydrogen bonds : angle 6.73598 ( 324) SS BOND : bond 0.00383 ( 5) SS BOND : angle 2.16497 ( 10) covalent geometry : bond 0.00502 ( 3413) covalent geometry : angle 0.63074 ( 4642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.709 Fit side-chains REVERT: B 406 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8515 (mt-10) REVERT: F 48 ILE cc_start: 0.8559 (mm) cc_final: 0.8323 (mm) REVERT: F 100 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7862 (tm-30) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.3728 time to fit residues: 26.7735 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.116895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097758 restraints weight = 5047.744| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.18 r_work: 0.3144 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3420 Z= 0.186 Angle : 0.640 11.015 4658 Z= 0.331 Chirality : 0.047 0.171 501 Planarity : 0.005 0.048 595 Dihedral : 5.192 21.408 510 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.50 % Allowed : 8.61 % Favored : 88.89 % 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: -1.58 (0.40), residues: 412 helix: -3.38 (0.68), residues: 28 sheet: 0.14 (0.45), residues: 147 loop : -1.57 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.021 0.002 PHE G 83 TYR 0.012 0.001 TYR B 453 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 1.55168 ( 3) link_BETA1-4 : bond 0.00219 ( 1) link_BETA1-4 : angle 1.13614 ( 3) hydrogen bonds : bond 0.03910 ( 104) hydrogen bonds : angle 6.03074 ( 324) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.68612 ( 10) covalent geometry : bond 0.00440 ( 3413) covalent geometry : angle 0.63455 ( 4642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.944 Fit side-chains REVERT: B 406 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8471 (mt-10) REVERT: B 417 LYS cc_start: 0.8666 (tppt) cc_final: 0.8341 (tptt) REVERT: F 48 ILE cc_start: 0.8572 (mm) cc_final: 0.8367 (mm) REVERT: F 100 ASP cc_start: 0.8843 (t0) cc_final: 0.8621 (t0) REVERT: F 100 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7801 (tm-30) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.3494 time to fit residues: 26.5731 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 39 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.118916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098385 restraints weight = 5141.541| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.40 r_work: 0.3152 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3420 Z= 0.127 Angle : 0.576 9.623 4658 Z= 0.297 Chirality : 0.045 0.158 501 Planarity : 0.004 0.046 595 Dihedral : 4.899 20.517 510 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.83 % Allowed : 11.67 % Favored : 87.50 % 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: -1.60 (0.39), residues: 412 helix: -2.91 (0.77), residues: 27 sheet: -0.06 (0.46), residues: 136 loop : -1.47 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE G 83 TYR 0.009 0.001 TYR G 91 ARG 0.003 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 1.30620 ( 3) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.01790 ( 3) hydrogen bonds : bond 0.03417 ( 104) hydrogen bonds : angle 5.64871 ( 324) SS BOND : bond 0.00747 ( 5) SS BOND : angle 1.23410 ( 10) covalent geometry : bond 0.00297 ( 3413) covalent geometry : angle 0.57244 ( 4642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.431 Fit side-chains REVERT: B 406 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8428 (mt-10) REVERT: B 417 LYS cc_start: 0.8647 (tppt) cc_final: 0.8314 (tptt) REVERT: F 99 GLU cc_start: 0.9019 (tt0) cc_final: 0.8764 (tt0) REVERT: F 100 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7567 (tm-30) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.2350 time to fit residues: 17.4184 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097816 restraints weight = 5111.912| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.42 r_work: 0.3140 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3420 Z= 0.150 Angle : 0.583 9.108 4658 Z= 0.302 Chirality : 0.045 0.163 501 Planarity : 0.004 0.044 595 Dihedral : 4.858 20.679 510 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.06 % Allowed : 11.11 % Favored : 85.83 % 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: -1.41 (0.40), residues: 412 helix: -2.97 (0.76), residues: 27 sheet: 0.18 (0.45), residues: 147 loop : -1.46 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE G 83 TYR 0.015 0.001 TYR F 100F ARG 0.002 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.38809 ( 3) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.05295 ( 3) hydrogen bonds : bond 0.03401 ( 104) hydrogen bonds : angle 5.54236 ( 324) SS BOND : bond 0.00802 ( 5) SS BOND : angle 1.28373 ( 10) covalent geometry : bond 0.00355 ( 3413) covalent geometry : angle 0.57930 ( 4642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.392 Fit side-chains REVERT: B 376 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 403 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7918 (mtp85) REVERT: B 406 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 417 LYS cc_start: 0.8648 (tppt) cc_final: 0.8215 (tppt) REVERT: F 100 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7621 (tm-30) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.1910 time to fit residues: 15.1367 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.118200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098190 restraints weight = 5226.469| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.31 r_work: 0.3146 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3420 Z= 0.159 Angle : 0.594 9.089 4658 Z= 0.308 Chirality : 0.046 0.167 501 Planarity : 0.004 0.044 595 Dihedral : 4.904 21.159 510 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.06 % Allowed : 11.67 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.40), residues: 412 helix: -2.97 (0.75), residues: 27 sheet: -0.05 (0.47), residues: 135 loop : -1.45 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE G 83 TYR 0.016 0.001 TYR F 100F ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 1.37807 ( 3) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 1.03781 ( 3) hydrogen bonds : bond 0.03390 ( 104) hydrogen bonds : angle 5.46313 ( 324) SS BOND : bond 0.00729 ( 5) SS BOND : angle 1.32494 ( 10) covalent geometry : bond 0.00376 ( 3413) covalent geometry : angle 0.59019 ( 4642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.390 Fit side-chains REVERT: B 376 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8719 (p) REVERT: B 406 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 417 LYS cc_start: 0.8668 (tppt) cc_final: 0.8271 (tppt) REVERT: F 82 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7712 (mp) REVERT: F 100 ASP cc_start: 0.8765 (t0) cc_final: 0.8556 (t0) REVERT: F 100 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7732 (tm-30) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.1920 time to fit residues: 14.1793 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.118567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098773 restraints weight = 5078.571| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.28 r_work: 0.3152 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3420 Z= 0.149 Angle : 0.593 8.754 4658 Z= 0.305 Chirality : 0.046 0.176 501 Planarity : 0.004 0.044 595 Dihedral : 4.859 21.257 510 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.06 % Allowed : 12.50 % Favored : 84.44 % 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: -1.55 (0.40), residues: 412 helix: -2.88 (0.77), residues: 27 sheet: 0.02 (0.47), residues: 136 loop : -1.46 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE G 83 TYR 0.016 0.001 TYR F 100F ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 1.34957 ( 3) link_BETA1-4 : bond 0.00297 ( 1) link_BETA1-4 : angle 1.02033 ( 3) hydrogen bonds : bond 0.03391 ( 104) hydrogen bonds : angle 5.41109 ( 324) SS BOND : bond 0.00743 ( 5) SS BOND : angle 1.33535 ( 10) covalent geometry : bond 0.00352 ( 3413) covalent geometry : angle 0.58896 ( 4642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.456 Fit side-chains REVERT: B 376 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8711 (p) REVERT: B 406 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8505 (mt-10) REVERT: B 417 LYS cc_start: 0.8665 (tppt) cc_final: 0.8276 (tppt) REVERT: F 82 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7726 (mp) REVERT: F 100 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7702 (tm-30) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.3426 time to fit residues: 26.1334 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 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 = 0.3540 r_free = 0.3540 target = 0.118343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098633 restraints weight = 5109.035| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.25 r_work: 0.3152 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3420 Z= 0.154 Angle : 0.603 8.368 4658 Z= 0.311 Chirality : 0.046 0.164 501 Planarity : 0.004 0.043 595 Dihedral : 4.891 22.937 510 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.06 % Allowed : 13.33 % Favored : 83.61 % 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: -1.48 (0.40), residues: 412 helix: -3.04 (0.74), residues: 28 sheet: -0.01 (0.47), residues: 136 loop : -1.32 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.017 0.002 PHE G 83 TYR 0.017 0.001 TYR F 100F ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 1.35708 ( 3) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 1.00905 ( 3) hydrogen bonds : bond 0.03310 ( 104) hydrogen bonds : angle 5.43160 ( 324) SS BOND : bond 0.00747 ( 5) SS BOND : angle 1.35069 ( 10) covalent geometry : bond 0.00362 ( 3413) covalent geometry : angle 0.59913 ( 4642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.621 Fit side-chains REVERT: B 376 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 406 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8497 (mt-10) REVERT: B 417 LYS cc_start: 0.8667 (tppt) cc_final: 0.8283 (tppt) REVERT: F 82 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (mp) REVERT: F 100 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7703 (tm-30) outliers start: 11 outliers final: 7 residues processed: 61 average time/residue: 0.2097 time to fit residues: 15.9213 Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.119842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100205 restraints weight = 5060.944| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.26 r_work: 0.3181 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3420 Z= 0.122 Angle : 0.574 7.710 4658 Z= 0.294 Chirality : 0.044 0.148 501 Planarity : 0.004 0.043 595 Dihedral : 4.762 25.604 510 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.50 % Allowed : 14.44 % Favored : 83.06 % 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: -1.33 (0.40), residues: 412 helix: -2.78 (0.89), residues: 22 sheet: 0.00 (0.47), residues: 137 loop : -1.24 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.001 PHE G 83 TYR 0.014 0.001 TYR F 100F ARG 0.005 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 1.21271 ( 3) link_BETA1-4 : bond 0.00322 ( 1) link_BETA1-4 : angle 0.95938 ( 3) hydrogen bonds : bond 0.03109 ( 104) hydrogen bonds : angle 5.35421 ( 324) SS BOND : bond 0.00714 ( 5) SS BOND : angle 1.29736 ( 10) covalent geometry : bond 0.00286 ( 3413) covalent geometry : angle 0.57052 ( 4642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.512 Fit side-chains REVERT: B 406 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8509 (mt-10) REVERT: B 417 LYS cc_start: 0.8642 (tppt) cc_final: 0.8260 (tppt) REVERT: F 82 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7726 (mp) REVERT: F 99 GLU cc_start: 0.8799 (tt0) cc_final: 0.8594 (tt0) REVERT: F 100 ASP cc_start: 0.8621 (t0) cc_final: 0.8412 (t0) REVERT: F 100 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7621 (tm-30) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.2565 time to fit residues: 18.7828 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.118722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099078 restraints weight = 5075.179| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.27 r_work: 0.3160 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3420 Z= 0.151 Angle : 0.607 8.098 4658 Z= 0.309 Chirality : 0.046 0.160 501 Planarity : 0.004 0.043 595 Dihedral : 4.877 25.834 510 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 15.28 % Favored : 82.22 % 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: -1.35 (0.40), residues: 412 helix: -2.87 (0.76), residues: 28 sheet: 0.05 (0.48), residues: 136 loop : -1.23 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.017 0.002 PHE G 83 TYR 0.016 0.001 TYR F 100F ARG 0.007 0.001 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 1.35634 ( 3) link_BETA1-4 : bond 0.00277 ( 1) link_BETA1-4 : angle 0.98374 ( 3) hydrogen bonds : bond 0.03193 ( 104) hydrogen bonds : angle 5.37292 ( 324) SS BOND : bond 0.00736 ( 5) SS BOND : angle 1.35602 ( 10) covalent geometry : bond 0.00358 ( 3413) covalent geometry : angle 0.60286 ( 4642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.433 Fit side-chains REVERT: B 376 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8731 (p) REVERT: B 406 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8508 (mt-10) REVERT: B 417 LYS cc_start: 0.8650 (tppt) cc_final: 0.8271 (tppt) REVERT: F 82 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7900 (mp) REVERT: F 99 GLU cc_start: 0.8816 (tt0) cc_final: 0.8592 (tt0) REVERT: F 100 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7647 (tm-30) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.3380 time to fit residues: 24.0366 Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.118511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098709 restraints weight = 5140.997| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.27 r_work: 0.3154 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3420 Z= 0.163 Angle : 0.609 8.262 4658 Z= 0.311 Chirality : 0.046 0.165 501 Planarity : 0.004 0.042 595 Dihedral : 4.950 26.402 510 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 15.56 % Favored : 81.94 % 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: -1.38 (0.40), residues: 412 helix: -2.92 (0.75), residues: 28 sheet: 0.05 (0.48), residues: 136 loop : -1.25 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE G 83 TYR 0.017 0.001 TYR F 100F ARG 0.006 0.001 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 1.40598 ( 3) link_BETA1-4 : bond 0.00254 ( 1) link_BETA1-4 : angle 0.99466 ( 3) hydrogen bonds : bond 0.03261 ( 104) hydrogen bonds : angle 5.40040 ( 324) SS BOND : bond 0.00737 ( 5) SS BOND : angle 1.43785 ( 10) covalent geometry : bond 0.00386 ( 3413) covalent geometry : angle 0.60443 ( 4642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.43 seconds wall clock time: 60 minutes 4.73 seconds (3604.73 seconds total)