Starting phenix.real_space_refine on Wed Jul 23 13:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8r_27255/07_2025/8d8r_27255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8r_27255/07_2025/8d8r_27255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2025/8d8r_27255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2025/8d8r_27255.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2025/8d8r_27255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2025/8d8r_27255.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.039 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 19 5.16 5 C 2102 2.51 5 N 562 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 3323 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} 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: 3.72, per 1000 atoms: 1.12 Number of scatterers: 3323 At special positions: 0 Unit cell: (69.564, 59.024, 102.238, 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 19 16.00 O 640 8.00 N 562 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 102 " distance=2.19 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.21 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 A1301 " - " ASN A 343 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 561.8 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 15.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.590A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.799A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.510A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.449A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.531A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.510A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.612A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 119 hydrogen bonds defined for protein. 267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 863 1.33 - 1.46: 844 1.46 - 1.58: 1674 1.58 - 1.71: 0 1.71 - 1.83: 24 Bond restraints: 3405 Sorted by residual: bond pdb=" CB PHE H 106 " pdb=" CG PHE H 106 " ideal model delta sigma weight residual 1.502 1.444 0.058 2.30e-02 1.89e+03 6.34e+00 bond pdb=" CG ASP L 82 " pdb=" OD2 ASP L 82 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 bond pdb=" CD GLU H 10 " pdb=" OE1 GLU H 10 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.46e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" CG ASP A 389 " pdb=" OD2 ASP A 389 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.29e+00 ... (remaining 3400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3935 1.62 - 3.24: 561 3.24 - 4.85: 95 4.85 - 6.47: 24 6.47 - 8.09: 7 Bond angle restraints: 4622 Sorted by residual: angle pdb=" C ALA H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 119.78 127.87 -8.09 1.03e+00 9.43e-01 6.17e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 119.76 127.18 -7.42 1.03e+00 9.43e-01 5.19e+01 angle pdb=" C ILE L 58 " pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 119.78 126.71 -6.93 1.03e+00 9.43e-01 4.53e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 126.31 -6.75 1.02e+00 9.61e-01 4.38e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 125.98 -6.42 1.02e+00 9.61e-01 3.96e+01 ... (remaining 4617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 1933 16.51 - 33.03: 61 33.03 - 49.54: 15 49.54 - 66.05: 7 66.05 - 82.56: 6 Dihedral angle restraints: 2022 sinusoidal: 798 harmonic: 1224 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.99 -52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 55.61 37.39 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA ALA H 94 " pdb=" C ALA H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 274 0.041 - 0.081: 153 0.081 - 0.122: 51 0.122 - 0.163: 16 0.163 - 0.203: 4 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN H 103 " pdb=" N ASN H 103 " pdb=" C ASN H 103 " pdb=" CB ASN H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.45e-01 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 2.47 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 495 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 423 " 0.045 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR A 423 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 423 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 423 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 423 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 423 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 423 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 423 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 78 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C LEU L 78 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU L 78 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU L 79 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 488 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C CYS A 488 " -0.033 2.00e-02 2.50e+03 pdb=" O CYS A 488 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 489 " 0.011 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1757 2.99 - 3.47: 2933 3.47 - 3.94: 5421 3.94 - 4.42: 6051 4.42 - 4.90: 9996 Nonbonded interactions: 26158 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.512 3.040 nonbonded pdb=" O LYS H 13 " pdb=" OG1 THR H 16 " model vdw 2.538 3.040 nonbonded pdb=" N TYR A 380 " pdb=" N GLY A 381 " model vdw 2.550 2.560 nonbonded pdb=" O SER H 31 " pdb=" OG SER H 101 " model vdw 2.554 3.040 nonbonded pdb=" OG SER H 98 " pdb=" N SER H 99 " model vdw 2.556 3.120 ... (remaining 26153 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 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 : 0.012 0.183 3412 Z= 0.636 Angle : 1.263 8.091 4637 Z= 0.872 Chirality : 0.056 0.203 498 Planarity : 0.006 0.024 596 Dihedral : 10.916 82.563 1228 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.96 (0.43), residues: 419 helix: -4.23 (0.36), residues: 34 sheet: 1.42 (0.42), residues: 150 loop : 2.42 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.016 0.004 PHE A 400 TYR 0.045 0.005 TYR A 423 ARG 0.003 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.07200 ( 1) link_NAG-ASN : angle 1.35761 ( 3) hydrogen bonds : bond 0.18158 ( 112) hydrogen bonds : angle 9.30121 ( 267) SS BOND : bond 0.10135 ( 6) SS BOND : angle 3.11307 ( 12) covalent geometry : bond 0.01100 ( 3405) covalent geometry : angle 1.25470 ( 4622) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.7054 (mm) cc_final: 0.6774 (mm) REVERT: H 20 VAL cc_start: 0.8368 (t) cc_final: 0.7917 (p) REVERT: H 57 THR cc_start: 0.6787 (p) cc_final: 0.6535 (t) REVERT: A 354 ASN cc_start: 0.7161 (t0) cc_final: 0.6751 (p0) REVERT: A 427 ASP cc_start: 0.8005 (m-30) cc_final: 0.7564 (p0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1713 time to fit residues: 25.3007 Evaluate side-chains 76 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.193651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170805 restraints weight = 6309.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175619 restraints weight = 4037.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.178936 restraints weight = 2832.471| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3412 Z= 0.182 Angle : 0.657 5.962 4637 Z= 0.363 Chirality : 0.044 0.130 498 Planarity : 0.005 0.059 596 Dihedral : 5.121 18.594 491 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.28 % Allowed : 1.39 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 419 helix: -3.63 (0.64), residues: 28 sheet: 0.86 (0.40), residues: 158 loop : 1.47 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP H 36 HIS 0.001 0.001 HIS L 90 PHE 0.039 0.003 PHE A 400 TYR 0.017 0.002 TYR A 453 ARG 0.004 0.001 ARG H 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 1) link_NAG-ASN : angle 1.47797 ( 3) hydrogen bonds : bond 0.04606 ( 112) hydrogen bonds : angle 6.97473 ( 267) SS BOND : bond 0.00427 ( 6) SS BOND : angle 0.45872 ( 12) covalent geometry : bond 0.00405 ( 3405) covalent geometry : angle 0.65628 ( 4622) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 VAL cc_start: 0.8711 (t) cc_final: 0.8478 (t) REVERT: H 36 TRP cc_start: 0.8543 (m100) cc_final: 0.8023 (m100) REVERT: H 80 MET cc_start: 0.4246 (ptm) cc_final: 0.3771 (ptm) REVERT: A 370 ASN cc_start: 0.7070 (m-40) cc_final: 0.6803 (p0) REVERT: A 403 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7428 (mtm110) REVERT: A 427 ASP cc_start: 0.8032 (m-30) cc_final: 0.7529 (p0) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1528 time to fit residues: 18.7991 Evaluate side-chains 84 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.188239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165313 restraints weight = 6116.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169779 restraints weight = 3940.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.172866 restraints weight = 2792.603| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3412 Z= 0.187 Angle : 0.653 8.971 4637 Z= 0.362 Chirality : 0.046 0.276 498 Planarity : 0.005 0.051 596 Dihedral : 5.356 26.669 491 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.55 % Allowed : 3.32 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.42), residues: 419 helix: -3.56 (0.65), residues: 28 sheet: 0.51 (0.39), residues: 160 loop : 0.78 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP L 96 HIS 0.002 0.001 HIS A 519 PHE 0.025 0.002 PHE A 400 TYR 0.021 0.002 TYR L 32 ARG 0.008 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 1) link_NAG-ASN : angle 1.62088 ( 3) hydrogen bonds : bond 0.03902 ( 112) hydrogen bonds : angle 6.85554 ( 267) SS BOND : bond 0.00996 ( 6) SS BOND : angle 1.57644 ( 12) covalent geometry : bond 0.00424 ( 3405) covalent geometry : angle 0.64730 ( 4622) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8726 (m100) cc_final: 0.8506 (m100) REVERT: H 79 TYR cc_start: 0.7360 (m-80) cc_final: 0.7076 (m-10) REVERT: H 80 MET cc_start: 0.4656 (ptm) cc_final: 0.3996 (ptm) REVERT: H 111 GLN cc_start: 0.7640 (pm20) cc_final: 0.7336 (pt0) outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.2554 time to fit residues: 29.5489 Evaluate side-chains 80 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.186160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162416 restraints weight = 6440.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166798 restraints weight = 4211.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169866 restraints weight = 3035.402| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3412 Z= 0.213 Angle : 0.674 7.505 4637 Z= 0.367 Chirality : 0.047 0.262 498 Planarity : 0.006 0.054 596 Dihedral : 5.770 32.473 491 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.28 % Allowed : 2.77 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.41), residues: 419 helix: -3.52 (0.65), residues: 28 sheet: 0.43 (0.41), residues: 152 loop : 0.30 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 96 HIS 0.002 0.001 HIS L 90 PHE 0.013 0.002 PHE H 29 TYR 0.027 0.002 TYR L 32 ARG 0.006 0.001 ARG H 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 1) link_NAG-ASN : angle 1.95882 ( 3) hydrogen bonds : bond 0.03918 ( 112) hydrogen bonds : angle 6.90601 ( 267) SS BOND : bond 0.01451 ( 6) SS BOND : angle 2.24798 ( 12) covalent geometry : bond 0.00489 ( 3405) covalent geometry : angle 0.66348 ( 4622) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8718 (m100) cc_final: 0.8505 (m100) REVERT: H 80 MET cc_start: 0.5162 (ptm) cc_final: 0.4589 (ptm) REVERT: H 111 GLN cc_start: 0.7719 (pm20) cc_final: 0.7399 (pt0) REVERT: A 516 GLU cc_start: 0.5683 (tt0) cc_final: 0.5472 (tt0) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.3052 time to fit residues: 34.2396 Evaluate side-chains 80 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.186642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163372 restraints weight = 6436.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167554 restraints weight = 4239.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.170529 restraints weight = 3070.831| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3412 Z= 0.179 Angle : 0.653 10.905 4637 Z= 0.355 Chirality : 0.046 0.267 498 Planarity : 0.005 0.049 596 Dihedral : 5.807 34.893 491 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.41), residues: 419 helix: -3.39 (0.69), residues: 28 sheet: 0.42 (0.42), residues: 150 loop : 0.04 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 96 HIS 0.007 0.003 HIS L 90 PHE 0.021 0.002 PHE H 29 TYR 0.018 0.002 TYR A 453 ARG 0.004 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 1) link_NAG-ASN : angle 3.75427 ( 3) hydrogen bonds : bond 0.03922 ( 112) hydrogen bonds : angle 6.78099 ( 267) SS BOND : bond 0.00639 ( 6) SS BOND : angle 1.57794 ( 12) covalent geometry : bond 0.00402 ( 3405) covalent geometry : angle 0.64198 ( 4622) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 91 TYR cc_start: 0.7469 (m-10) cc_final: 0.6812 (m-10) REVERT: H 30 MET cc_start: 0.8490 (mtp) cc_final: 0.8048 (mmm) REVERT: H 36 TRP cc_start: 0.8708 (m100) cc_final: 0.8228 (m100) REVERT: H 111 GLN cc_start: 0.7835 (pm20) cc_final: 0.7499 (pt0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1862 time to fit residues: 21.4234 Evaluate side-chains 80 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.187458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.164719 restraints weight = 6543.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169029 restraints weight = 4196.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172003 restraints weight = 2996.535| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3412 Z= 0.159 Angle : 0.624 9.264 4637 Z= 0.341 Chirality : 0.046 0.212 498 Planarity : 0.005 0.050 596 Dihedral : 5.746 34.730 491 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.41), residues: 419 helix: -3.19 (0.73), residues: 28 sheet: 0.37 (0.42), residues: 146 loop : -0.14 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 96 HIS 0.004 0.002 HIS L 90 PHE 0.028 0.002 PHE H 29 TYR 0.024 0.002 TYR A 453 ARG 0.005 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 1) link_NAG-ASN : angle 2.73730 ( 3) hydrogen bonds : bond 0.03758 ( 112) hydrogen bonds : angle 6.69344 ( 267) SS BOND : bond 0.01233 ( 6) SS BOND : angle 1.26060 ( 12) covalent geometry : bond 0.00357 ( 3405) covalent geometry : angle 0.61802 ( 4622) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8329 (m100) cc_final: 0.7950 (m100) REVERT: H 111 GLN cc_start: 0.7954 (pm20) cc_final: 0.7441 (pt0) REVERT: A 473 TYR cc_start: 0.8199 (t80) cc_final: 0.7948 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2596 time to fit residues: 28.5937 Evaluate side-chains 78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 20 optimal weight: 0.0970 chunk 35 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.193400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170287 restraints weight = 6371.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174523 restraints weight = 4155.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177490 restraints weight = 3015.199| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3412 Z= 0.119 Angle : 0.606 8.853 4637 Z= 0.329 Chirality : 0.047 0.186 498 Planarity : 0.005 0.050 596 Dihedral : 5.170 25.361 491 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.41), residues: 419 helix: -2.95 (0.80), residues: 28 sheet: 0.62 (0.45), residues: 134 loop : -0.15 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP H 50 HIS 0.003 0.001 HIS L 90 PHE 0.025 0.002 PHE H 29 TYR 0.027 0.002 TYR A 495 ARG 0.005 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 1) link_NAG-ASN : angle 2.58737 ( 3) hydrogen bonds : bond 0.03591 ( 112) hydrogen bonds : angle 6.49672 ( 267) SS BOND : bond 0.00590 ( 6) SS BOND : angle 1.06653 ( 12) covalent geometry : bond 0.00255 ( 3405) covalent geometry : angle 0.60050 ( 4622) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8128 (m100) cc_final: 0.7827 (m100) REVERT: H 111 GLN cc_start: 0.7815 (pm20) cc_final: 0.7253 (pt0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2208 time to fit residues: 25.8145 Evaluate side-chains 76 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.4220 r_free = 0.4220 target = 0.188499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165316 restraints weight = 6194.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169696 restraints weight = 3977.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.172772 restraints weight = 2839.528| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3412 Z= 0.150 Angle : 0.611 8.484 4637 Z= 0.335 Chirality : 0.047 0.193 498 Planarity : 0.005 0.048 596 Dihedral : 5.297 24.783 491 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.42), residues: 419 helix: -3.07 (0.78), residues: 28 sheet: 0.65 (0.44), residues: 136 loop : -0.19 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 50 HIS 0.002 0.001 HIS L 90 PHE 0.032 0.002 PHE A 400 TYR 0.027 0.002 TYR A 453 ARG 0.004 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 1) link_NAG-ASN : angle 2.26348 ( 3) hydrogen bonds : bond 0.03640 ( 112) hydrogen bonds : angle 6.58481 ( 267) SS BOND : bond 0.00713 ( 6) SS BOND : angle 1.01957 ( 12) covalent geometry : bond 0.00330 ( 3405) covalent geometry : angle 0.60742 ( 4622) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: H 30 MET cc_start: 0.8926 (mmm) cc_final: 0.8635 (mmm) REVERT: H 36 TRP cc_start: 0.8383 (m100) cc_final: 0.7908 (m100) REVERT: H 80 MET cc_start: 0.4387 (ptm) cc_final: 0.4090 (ptp) REVERT: H 111 GLN cc_start: 0.7760 (pm20) cc_final: 0.7442 (pt0) REVERT: A 473 TYR cc_start: 0.8299 (t80) cc_final: 0.7997 (t80) REVERT: A 516 GLU cc_start: 0.6032 (tt0) cc_final: 0.5501 (tt0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3311 time to fit residues: 35.9642 Evaluate side-chains 74 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.4226 r_free = 0.4226 target = 0.189008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165868 restraints weight = 6331.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170227 restraints weight = 4144.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.173305 restraints weight = 2980.565| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.8166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3412 Z= 0.146 Angle : 0.632 8.268 4637 Z= 0.336 Chirality : 0.047 0.199 498 Planarity : 0.005 0.048 596 Dihedral : 5.490 32.127 491 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.41), residues: 419 helix: -3.03 (0.79), residues: 28 sheet: 0.60 (0.44), residues: 136 loop : -0.22 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 50 HIS 0.002 0.001 HIS L 90 PHE 0.018 0.002 PHE A 400 TYR 0.024 0.002 TYR A 453 ARG 0.006 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 1) link_NAG-ASN : angle 2.20540 ( 3) hydrogen bonds : bond 0.03508 ( 112) hydrogen bonds : angle 6.55798 ( 267) SS BOND : bond 0.00680 ( 6) SS BOND : angle 0.97008 ( 12) covalent geometry : bond 0.00329 ( 3405) covalent geometry : angle 0.62878 ( 4622) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8386 (m100) cc_final: 0.7877 (m100) REVERT: H 80 MET cc_start: 0.4384 (ptm) cc_final: 0.4148 (ptp) REVERT: H 111 GLN cc_start: 0.7791 (pm20) cc_final: 0.7399 (pt0) REVERT: A 473 TYR cc_start: 0.8291 (t80) cc_final: 0.7556 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1850 time to fit residues: 18.3600 Evaluate side-chains 73 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.4243 r_free = 0.4243 target = 0.190984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.167979 restraints weight = 6301.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172235 restraints weight = 4086.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175384 restraints weight = 2930.343| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3412 Z= 0.125 Angle : 0.610 7.798 4637 Z= 0.323 Chirality : 0.047 0.250 498 Planarity : 0.004 0.046 596 Dihedral : 5.254 30.884 491 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.42), residues: 419 helix: -2.92 (0.83), residues: 28 sheet: 0.61 (0.44), residues: 136 loop : -0.27 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 50 HIS 0.003 0.001 HIS L 90 PHE 0.016 0.001 PHE H 29 TYR 0.021 0.002 TYR H 59 ARG 0.006 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 1) link_NAG-ASN : angle 2.28459 ( 3) hydrogen bonds : bond 0.03482 ( 112) hydrogen bonds : angle 6.38996 ( 267) SS BOND : bond 0.00702 ( 6) SS BOND : angle 0.88933 ( 12) covalent geometry : bond 0.00278 ( 3405) covalent geometry : angle 0.60657 ( 4622) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8334 (m100) cc_final: 0.7932 (m100) REVERT: H 80 MET cc_start: 0.4357 (ptm) cc_final: 0.4040 (ptp) REVERT: H 111 GLN cc_start: 0.7802 (pm20) cc_final: 0.7384 (pt0) REVERT: A 473 TYR cc_start: 0.8275 (t80) cc_final: 0.8030 (t80) REVERT: A 509 ARG cc_start: 0.8185 (ptm-80) cc_final: 0.7955 (tmm160) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1574 time to fit residues: 15.7778 Evaluate side-chains 72 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 5 optimal weight: 0.0370 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.4258 r_free = 0.4258 target = 0.191964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169103 restraints weight = 6325.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.173290 restraints weight = 4186.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176327 restraints weight = 3034.478| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.8361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3412 Z= 0.125 Angle : 0.589 7.350 4637 Z= 0.316 Chirality : 0.046 0.214 498 Planarity : 0.005 0.049 596 Dihedral : 5.259 31.047 491 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.42), residues: 419 helix: -2.92 (0.82), residues: 28 sheet: 0.63 (0.44), residues: 136 loop : -0.36 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP H 50 HIS 0.002 0.001 HIS L 90 PHE 0.020 0.002 PHE A 400 TYR 0.019 0.001 TYR A 453 ARG 0.005 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 1) link_NAG-ASN : angle 2.31556 ( 3) hydrogen bonds : bond 0.03409 ( 112) hydrogen bonds : angle 6.26827 ( 267) SS BOND : bond 0.00699 ( 6) SS BOND : angle 0.83771 ( 12) covalent geometry : bond 0.00278 ( 3405) covalent geometry : angle 0.58566 ( 4622) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.04 seconds wall clock time: 42 minutes 9.67 seconds (2529.67 seconds total)