Starting phenix.real_space_refine on Wed Jul 23 17:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkm_23899/07_2025/7mkm_23899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkm_23899/07_2025/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2025/7mkm_23899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2025/7mkm_23899.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2025/7mkm_23899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2025/7mkm_23899.cif" } resolution = 3.16 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.54, per 1000 atoms: 1.74 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 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 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 560.5 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 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: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 198 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: 1.26 Time building geometry restraints manager: 1.33 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: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4317 2.13 - 4.25: 132 4.25 - 6.38: 4 6.38 - 8.50: 2 8.50 - 10.63: 2 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1753 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1935 sinusoidal: 758 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 312 0.037 - 0.074: 113 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 3.120 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 3.040 ... (remaining 22448 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: 70.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 21.170 Find NCS groups from input model: 0.040 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:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 : 0.003 0.031 3282 Z= 0.131 Angle : 0.806 10.631 4470 Z= 0.434 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.042 88.529 1176 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 429 TYR 0.018 0.003 TYR L 85 ARG 0.014 0.002 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 5.05605 ( 3) hydrogen bonds : bond 0.30388 ( 72) hydrogen bonds : angle 12.10241 ( 198) SS BOND : bond 0.00488 ( 5) SS BOND : angle 1.19163 ( 10) covalent geometry : bond 0.00263 ( 3276) covalent geometry : angle 0.79467 ( 4457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.625 Fit side-chains REVERT: A 486 PHE cc_start: 0.6384 (t80) cc_final: 0.6143 (t80) REVERT: L 34 TRP cc_start: 0.4286 (m100) cc_final: 0.4080 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3327 time to fit residues: 24.0553 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 15 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.201145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178302 restraints weight = 5163.190| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.97 r_work: 0.4331 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3282 Z= 0.139 Angle : 0.717 8.076 4470 Z= 0.388 Chirality : 0.046 0.251 480 Planarity : 0.005 0.054 572 Dihedral : 7.546 26.259 471 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.39), residues: 400 helix: -2.27 (0.88), residues: 26 sheet: 1.58 (0.46), residues: 113 loop : -1.74 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.030 0.002 PHE A 400 TYR 0.026 0.002 TYR A 423 ARG 0.002 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 1) link_NAG-ASN : angle 2.91437 ( 3) hydrogen bonds : bond 0.04570 ( 72) hydrogen bonds : angle 8.90264 ( 198) SS BOND : bond 0.00595 ( 5) SS BOND : angle 1.19720 ( 10) covalent geometry : bond 0.00280 ( 3276) covalent geometry : angle 0.71135 ( 4457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.338 Fit side-chains REVERT: A 365 TYR cc_start: 0.6380 (m-80) cc_final: 0.5722 (m-80) REVERT: A 410 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 465 GLU cc_start: 0.6824 (tp30) cc_final: 0.6391 (tp30) REVERT: A 466 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7331 (mtm-85) REVERT: A 486 PHE cc_start: 0.7038 (t80) cc_final: 0.6543 (t80) REVERT: L 86 TYR cc_start: 0.5469 (m-10) cc_final: 0.5105 (m-10) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1982 time to fit residues: 13.7950 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.193558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.172202 restraints weight = 5111.367| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.70 r_work: 0.4280 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3282 Z= 0.161 Angle : 0.707 8.473 4470 Z= 0.384 Chirality : 0.047 0.312 480 Planarity : 0.005 0.053 572 Dihedral : 7.145 27.626 471 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.01 % Allowed : 13.22 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.26 (0.39), residues: 400 helix: -1.88 (1.03), residues: 26 sheet: 1.06 (0.44), residues: 115 loop : -1.75 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.002 PHE A 400 TYR 0.014 0.002 TYR H 59 ARG 0.003 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 1) link_NAG-ASN : angle 2.72465 ( 3) hydrogen bonds : bond 0.05121 ( 72) hydrogen bonds : angle 8.07012 ( 198) SS BOND : bond 0.00586 ( 5) SS BOND : angle 1.08570 ( 10) covalent geometry : bond 0.00342 ( 3276) covalent geometry : angle 0.70244 ( 4457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.347 Fit side-chains REVERT: A 410 ILE cc_start: 0.8338 (mm) cc_final: 0.7846 (mm) REVERT: A 465 GLU cc_start: 0.7122 (tp30) cc_final: 0.6749 (tp30) REVERT: A 466 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: A 486 PHE cc_start: 0.6936 (t80) cc_final: 0.6538 (t80) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.2537 time to fit residues: 16.7722 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.191997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170954 restraints weight = 5167.253| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.69 r_work: 0.4263 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3282 Z= 0.165 Angle : 0.700 8.327 4470 Z= 0.380 Chirality : 0.046 0.280 480 Planarity : 0.005 0.055 572 Dihedral : 6.909 27.905 471 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.44 % Allowed : 14.08 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.62 (0.39), residues: 400 helix: -1.87 (1.03), residues: 26 sheet: 0.41 (0.44), residues: 113 loop : -1.79 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.002 PHE A 400 TYR 0.015 0.002 TYR H 58 ARG 0.002 0.000 ARG H 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 2.65823 ( 3) hydrogen bonds : bond 0.04733 ( 72) hydrogen bonds : angle 7.82232 ( 198) SS BOND : bond 0.00568 ( 5) SS BOND : angle 1.09177 ( 10) covalent geometry : bond 0.00352 ( 3276) covalent geometry : angle 0.69527 ( 4457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.308 Fit side-chains REVERT: A 410 ILE cc_start: 0.8374 (mm) cc_final: 0.8077 (mm) REVERT: A 465 GLU cc_start: 0.7114 (tp30) cc_final: 0.6825 (tp30) REVERT: A 466 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7308 (mtm-85) REVERT: A 486 PHE cc_start: 0.6813 (t80) cc_final: 0.6472 (t80) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1818 time to fit residues: 11.5414 Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.0770 chunk 30 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.192623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.170990 restraints weight = 5186.689| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.84 r_work: 0.4264 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3282 Z= 0.138 Angle : 0.664 8.165 4470 Z= 0.359 Chirality : 0.045 0.252 480 Planarity : 0.005 0.051 572 Dihedral : 6.551 27.511 471 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 15.52 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.79 (0.39), residues: 400 helix: -1.85 (1.03), residues: 26 sheet: 0.23 (0.47), residues: 110 loop : -1.87 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.002 PHE A 400 TYR 0.012 0.002 TYR A 453 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 2.48558 ( 3) hydrogen bonds : bond 0.04345 ( 72) hydrogen bonds : angle 7.60331 ( 198) SS BOND : bond 0.00498 ( 5) SS BOND : angle 1.02658 ( 10) covalent geometry : bond 0.00289 ( 3276) covalent geometry : angle 0.66035 ( 4457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.354 Fit side-chains REVERT: A 410 ILE cc_start: 0.8294 (mm) cc_final: 0.7997 (mm) REVERT: A 465 GLU cc_start: 0.7076 (tp30) cc_final: 0.6810 (tp30) REVERT: A 466 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7327 (mtm180) REVERT: A 486 PHE cc_start: 0.6776 (t80) cc_final: 0.6476 (t80) REVERT: A 509 ARG cc_start: 0.6956 (mtt180) cc_final: 0.5936 (mtp85) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.1983 time to fit residues: 12.4324 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.191870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.170499 restraints weight = 5287.536| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.79 r_work: 0.4260 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3282 Z= 0.152 Angle : 0.673 8.186 4470 Z= 0.364 Chirality : 0.045 0.247 480 Planarity : 0.005 0.050 572 Dihedral : 6.468 27.248 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 16.38 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.93 (0.39), residues: 400 helix: -2.04 (1.00), residues: 27 sheet: 0.26 (0.50), residues: 99 loop : -1.93 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 400 TYR 0.014 0.002 TYR H 58 ARG 0.002 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 2.63139 ( 3) hydrogen bonds : bond 0.04523 ( 72) hydrogen bonds : angle 7.54193 ( 198) SS BOND : bond 0.00528 ( 5) SS BOND : angle 1.08012 ( 10) covalent geometry : bond 0.00323 ( 3276) covalent geometry : angle 0.66817 ( 4457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.340 Fit side-chains REVERT: A 410 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8011 (mm) REVERT: A 417 LYS cc_start: 0.5831 (mmtt) cc_final: 0.5620 (mmtt) REVERT: A 465 GLU cc_start: 0.7034 (tp30) cc_final: 0.6810 (tp30) REVERT: A 466 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7350 (mtm180) REVERT: A 486 PHE cc_start: 0.6724 (t80) cc_final: 0.6411 (t80) REVERT: A 509 ARG cc_start: 0.6974 (mtt180) cc_final: 0.5978 (mtp85) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.2042 time to fit residues: 12.6958 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.190623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.169340 restraints weight = 5134.060| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.76 r_work: 0.4245 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3282 Z= 0.170 Angle : 0.708 8.216 4470 Z= 0.382 Chirality : 0.046 0.248 480 Planarity : 0.005 0.050 572 Dihedral : 6.505 27.043 471 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.59 % Allowed : 16.38 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.39), residues: 400 helix: -2.07 (1.00), residues: 27 sheet: -0.04 (0.49), residues: 104 loop : -2.01 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.002 PHE A 347 TYR 0.020 0.002 TYR L 35 ARG 0.003 0.001 ARG L 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 1) link_NAG-ASN : angle 2.71258 ( 3) hydrogen bonds : bond 0.04769 ( 72) hydrogen bonds : angle 7.65963 ( 198) SS BOND : bond 0.00561 ( 5) SS BOND : angle 1.18808 ( 10) covalent geometry : bond 0.00369 ( 3276) covalent geometry : angle 0.70333 ( 4457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.332 Fit side-chains REVERT: A 410 ILE cc_start: 0.8415 (mm) cc_final: 0.8088 (mm) REVERT: A 417 LYS cc_start: 0.5739 (mmtt) cc_final: 0.5530 (mmtm) REVERT: A 486 PHE cc_start: 0.6722 (t80) cc_final: 0.6421 (t80) REVERT: A 509 ARG cc_start: 0.7057 (mtt180) cc_final: 0.6056 (mtp85) REVERT: H 103 ASP cc_start: 0.7633 (t0) cc_final: 0.7327 (m-30) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.1708 time to fit residues: 12.1467 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.0870 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.192433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.171313 restraints weight = 5171.227| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.76 r_work: 0.4267 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3282 Z= 0.134 Angle : 0.684 8.007 4470 Z= 0.367 Chirality : 0.045 0.211 480 Planarity : 0.005 0.048 572 Dihedral : 6.162 26.696 471 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.30 % Allowed : 17.82 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.08 (0.40), residues: 400 helix: -2.21 (0.87), residues: 33 sheet: 0.04 (0.51), residues: 100 loop : -1.96 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE A 400 TYR 0.017 0.002 TYR L 35 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 2.36489 ( 3) hydrogen bonds : bond 0.04128 ( 72) hydrogen bonds : angle 7.49135 ( 198) SS BOND : bond 0.00447 ( 5) SS BOND : angle 1.08705 ( 10) covalent geometry : bond 0.00288 ( 3276) covalent geometry : angle 0.67996 ( 4457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.355 Fit side-chains REVERT: A 410 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 417 LYS cc_start: 0.5769 (mmtt) cc_final: 0.5453 (mmtt) REVERT: A 465 GLU cc_start: 0.6811 (tp30) cc_final: 0.6510 (tp30) REVERT: A 466 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7385 (mtm-85) REVERT: A 486 PHE cc_start: 0.6579 (t80) cc_final: 0.6324 (t80) REVERT: A 509 ARG cc_start: 0.6940 (mtt180) cc_final: 0.6008 (mtp180) REVERT: H 103 ASP cc_start: 0.7731 (t0) cc_final: 0.7431 (m-30) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.1874 time to fit residues: 12.3282 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.191622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.170488 restraints weight = 5181.476| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.76 r_work: 0.4259 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3282 Z= 0.147 Angle : 0.688 7.930 4470 Z= 0.370 Chirality : 0.045 0.199 480 Planarity : 0.005 0.049 572 Dihedral : 6.097 24.689 471 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.87 % Allowed : 18.10 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.13 (0.40), residues: 400 helix: -2.26 (0.86), residues: 33 sheet: -0.13 (0.52), residues: 102 loop : -1.94 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 400 TYR 0.017 0.002 TYR L 35 ARG 0.002 0.000 ARG L 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 2.43664 ( 3) hydrogen bonds : bond 0.04318 ( 72) hydrogen bonds : angle 7.48785 ( 198) SS BOND : bond 0.00508 ( 5) SS BOND : angle 1.09720 ( 10) covalent geometry : bond 0.00318 ( 3276) covalent geometry : angle 0.68448 ( 4457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.326 Fit side-chains REVERT: A 410 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8057 (mm) REVERT: A 417 LYS cc_start: 0.5637 (mmtt) cc_final: 0.5431 (mmtm) REVERT: A 466 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: A 486 PHE cc_start: 0.6648 (t80) cc_final: 0.6380 (t80) REVERT: A 509 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6019 (mtp180) REVERT: H 103 ASP cc_start: 0.7729 (t0) cc_final: 0.7427 (t0) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.1934 time to fit residues: 12.5253 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.191722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.170366 restraints weight = 5128.982| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.85 r_work: 0.4255 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3282 Z= 0.143 Angle : 0.695 8.314 4470 Z= 0.372 Chirality : 0.045 0.178 480 Planarity : 0.005 0.048 572 Dihedral : 6.117 25.941 471 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.01 % Allowed : 19.54 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.14 (0.40), residues: 400 helix: -2.25 (0.86), residues: 33 sheet: -0.13 (0.52), residues: 102 loop : -1.95 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 400 TYR 0.015 0.002 TYR L 35 ARG 0.007 0.001 ARG L 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 2.26939 ( 3) hydrogen bonds : bond 0.04151 ( 72) hydrogen bonds : angle 7.54770 ( 198) SS BOND : bond 0.00465 ( 5) SS BOND : angle 1.08157 ( 10) covalent geometry : bond 0.00310 ( 3276) covalent geometry : angle 0.69132 ( 4457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.376 Fit side-chains REVERT: A 408 ARG cc_start: 0.8104 (ptt90) cc_final: 0.7747 (ptm-80) REVERT: A 410 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 417 LYS cc_start: 0.5651 (mmtt) cc_final: 0.5440 (mmtm) REVERT: A 486 PHE cc_start: 0.6582 (t80) cc_final: 0.6358 (t80) REVERT: A 509 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6036 (mtp180) REVERT: H 103 ASP cc_start: 0.7776 (t0) cc_final: 0.7429 (m-30) outliers start: 7 outliers final: 6 residues processed: 50 average time/residue: 0.2052 time to fit residues: 12.2507 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 23 optimal weight: 0.2980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.191469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.170164 restraints weight = 5206.862| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.86 r_work: 0.4251 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3282 Z= 0.145 Angle : 0.689 8.306 4470 Z= 0.369 Chirality : 0.044 0.171 480 Planarity : 0.005 0.048 572 Dihedral : 6.072 25.553 471 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.72 % Allowed : 19.83 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.14 (0.41), residues: 400 helix: -2.24 (0.87), residues: 33 sheet: -0.16 (0.53), residues: 102 loop : -1.95 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 400 TYR 0.016 0.002 TYR L 35 ARG 0.007 0.001 ARG L 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 2.19537 ( 3) hydrogen bonds : bond 0.04209 ( 72) hydrogen bonds : angle 7.54989 ( 198) SS BOND : bond 0.00488 ( 5) SS BOND : angle 1.07954 ( 10) covalent geometry : bond 0.00315 ( 3276) covalent geometry : angle 0.68540 ( 4457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.32 seconds wall clock time: 42 minutes 33.53 seconds (2553.53 seconds total)