Starting phenix.real_space_refine on Wed Mar 5 19:40:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8r_27255/03_2025/8d8r_27255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8r_27255/03_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_27255/03_2025/8d8r_27255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_2025/8d8r_27255.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_2025/8d8r_27255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_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-5624/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: 0.80 Conformation dependent library (CDL) restraints added in 404.8 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: 0.52 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: 0.89 Time building geometry restraints manager: 0.97 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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- 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 : 0.011 0.076 3405 Z= 0.717 Angle : 1.255 8.091 4622 Z= 0.870 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 *********************** 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 : 0.378 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: 0.1854 time to fit residues: 27.4481 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 : 0.352 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.193856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171072 restraints weight = 6299.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175734 restraints weight = 4013.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179052 restraints weight = 2824.923| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3405 Z= 0.263 Angle : 0.646 5.859 4622 Z= 0.356 Chirality : 0.044 0.130 498 Planarity : 0.005 0.062 596 Dihedral : 5.126 18.786 491 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.28 % Allowed : 1.94 % 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: 1.09 (0.42), residues: 419 helix: -3.73 (0.61), residues: 28 sheet: 0.83 (0.40), residues: 158 loop : 1.47 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.035 0.003 PHE A 400 TYR 0.018 0.002 TYR A 453 ARG 0.004 0.001 ARG A 403 *********************** 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 100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8498 (m100) cc_final: 0.7938 (m100) REVERT: A 403 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7275 (mtm110) REVERT: A 427 ASP cc_start: 0.8030 (m-30) cc_final: 0.7541 (p0) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1548 time to fit residues: 18.7511 Evaluate side-chains 85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.194524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172357 restraints weight = 6066.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.176936 restraints weight = 3878.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.180200 restraints weight = 2723.227| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3405 Z= 0.197 Angle : 0.559 5.284 4622 Z= 0.311 Chirality : 0.043 0.131 498 Planarity : 0.005 0.055 596 Dihedral : 4.656 18.327 491 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.28 % Allowed : 2.49 % Favored : 97.23 % 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: 0.63 (0.41), residues: 419 helix: -3.60 (0.63), residues: 28 sheet: 0.51 (0.39), residues: 151 loop : 1.08 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.035 0.002 PHE H 29 TYR 0.016 0.002 TYR A 473 ARG 0.003 0.000 ARG A 509 *********************** 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 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8235 (m100) cc_final: 0.7778 (m100) REVERT: H 111 GLN cc_start: 0.7322 (pm20) cc_final: 0.7098 (pt0) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1423 time to fit residues: 16.3772 Evaluate side-chains 82 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.185458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161286 restraints weight = 6487.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.165731 restraints weight = 4256.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168933 restraints weight = 3057.638| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3405 Z= 0.328 Angle : 0.710 10.579 4622 Z= 0.391 Chirality : 0.048 0.283 498 Planarity : 0.006 0.061 596 Dihedral : 5.948 33.927 491 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: -0.01 (0.41), residues: 419 helix: -3.59 (0.65), residues: 28 sheet: 0.23 (0.39), residues: 153 loop : 0.45 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP L 96 HIS 0.002 0.001 HIS L 90 PHE 0.034 0.003 PHE A 400 TYR 0.029 0.003 TYR L 32 ARG 0.012 0.001 ARG A 346 *********************** 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 96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8612 (m100) cc_final: 0.8409 (m100) REVERT: H 50 TRP cc_start: 0.7321 (p-90) cc_final: 0.7050 (p-90) REVERT: H 73 MET cc_start: 0.8420 (mmm) cc_final: 0.7825 (mmm) REVERT: H 79 TYR cc_start: 0.7178 (m-80) cc_final: 0.6914 (m-10) REVERT: H 80 MET cc_start: 0.5159 (mtm) cc_final: 0.4932 (mtp) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1740 time to fit residues: 19.8360 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 : 0.347 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.189370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166587 restraints weight = 6431.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.171028 restraints weight = 4239.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.174139 restraints weight = 3037.355| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3405 Z= 0.234 Angle : 0.682 16.411 4622 Z= 0.368 Chirality : 0.049 0.366 498 Planarity : 0.005 0.058 596 Dihedral : 5.440 33.681 491 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.28 % Allowed : 0.83 % 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: -0.02 (0.41), residues: 419 helix: -3.44 (0.76), residues: 28 sheet: 0.47 (0.40), residues: 151 loop : 0.23 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 96 HIS 0.002 0.001 HIS L 90 PHE 0.022 0.002 PHE H 29 TYR 0.023 0.002 TYR A 380 ARG 0.005 0.001 ARG A 346 *********************** 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 89 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 VAL cc_start: 0.8857 (t) cc_final: 0.8437 (t) REVERT: H 36 TRP cc_start: 0.8358 (m100) cc_final: 0.8150 (m100) REVERT: H 39 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6970 (tm-30) REVERT: H 45 LEU cc_start: 0.8643 (mt) cc_final: 0.8327 (mt) REVERT: H 50 TRP cc_start: 0.7464 (p-90) cc_final: 0.6992 (p-90) REVERT: H 80 MET cc_start: 0.4658 (mtm) cc_final: 0.4249 (ptm) REVERT: A 473 TYR cc_start: 0.8422 (t80) cc_final: 0.7963 (t80) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1425 time to fit residues: 15.7774 Evaluate side-chains 82 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 0.8980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.188434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165625 restraints weight = 6607.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.169868 restraints weight = 4360.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172918 restraints weight = 3146.261| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3405 Z= 0.242 Angle : 0.689 14.630 4622 Z= 0.368 Chirality : 0.048 0.319 498 Planarity : 0.005 0.053 596 Dihedral : 5.760 37.111 491 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % 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: -0.13 (0.41), residues: 419 helix: -3.54 (0.73), residues: 28 sheet: 0.59 (0.42), residues: 131 loop : 0.04 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 96 HIS 0.004 0.002 HIS L 90 PHE 0.036 0.002 PHE A 400 TYR 0.031 0.002 TYR A 380 ARG 0.004 0.001 ARG L 54 *********************** 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 94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7122 (tm-30) REVERT: H 50 TRP cc_start: 0.7918 (p-90) cc_final: 0.7345 (p-90) REVERT: A 473 TYR cc_start: 0.8465 (t80) cc_final: 0.8038 (t80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1421 time to fit residues: 16.6996 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 : 0.393 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** H 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.184184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161441 restraints weight = 6497.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165744 restraints weight = 4248.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168795 restraints weight = 3062.840| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3405 Z= 0.331 Angle : 0.742 15.303 4622 Z= 0.402 Chirality : 0.051 0.309 498 Planarity : 0.006 0.071 596 Dihedral : 6.537 36.203 491 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.28 % Allowed : 2.22 % Favored : 97.51 % 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: -0.63 (0.42), residues: 419 helix: -3.74 (0.62), residues: 34 sheet: 0.54 (0.44), residues: 129 loop : -0.40 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP H 36 HIS 0.003 0.002 HIS A 519 PHE 0.015 0.002 PHE A 400 TYR 0.029 0.003 TYR A 453 ARG 0.004 0.001 ARG L 61 *********************** 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 96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8515 (m100) cc_final: 0.8299 (m100) REVERT: H 50 TRP cc_start: 0.8062 (p-90) cc_final: 0.7378 (p-90) REVERT: H 52 VAL cc_start: 0.8792 (t) cc_final: 0.8528 (t) REVERT: A 351 TYR cc_start: 0.7730 (p90) cc_final: 0.7460 (p90) REVERT: A 375 SER cc_start: 0.8944 (p) cc_final: 0.8682 (t) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1631 time to fit residues: 18.6801 Evaluate side-chains 82 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.0670 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 37 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.1932 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.191183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169208 restraints weight = 6501.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173491 restraints weight = 4255.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176452 restraints weight = 3064.347| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3405 Z= 0.169 Angle : 0.649 12.175 4622 Z= 0.341 Chirality : 0.048 0.269 498 Planarity : 0.005 0.068 596 Dihedral : 5.305 25.688 491 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % 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: -0.30 (0.42), residues: 419 helix: -3.54 (0.69), residues: 34 sheet: 0.93 (0.45), residues: 129 loop : -0.27 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.001 0.001 HIS L 90 PHE 0.010 0.001 PHE H 27 TYR 0.023 0.002 TYR H 59 ARG 0.004 0.001 ARG L 45 *********************** 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 92 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6697 (tm-30) REVERT: H 50 TRP cc_start: 0.7738 (p-90) cc_final: 0.7032 (p-90) REVERT: H 52 VAL cc_start: 0.8773 (t) cc_final: 0.8446 (t) REVERT: H 79 TYR cc_start: 0.7189 (m-10) cc_final: 0.6919 (m-10) REVERT: A 375 SER cc_start: 0.8987 (p) cc_final: 0.8766 (t) REVERT: A 516 GLU cc_start: 0.6104 (tt0) cc_final: 0.5728 (tt0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1444 time to fit residues: 16.3741 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 : 0.334 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.188428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.166487 restraints weight = 6534.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170664 restraints weight = 4328.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173586 restraints weight = 3147.526| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.8413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3405 Z= 0.245 Angle : 0.672 11.791 4622 Z= 0.358 Chirality : 0.049 0.280 498 Planarity : 0.005 0.071 596 Dihedral : 5.680 34.538 491 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % 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: -0.53 (0.42), residues: 419 helix: -3.64 (0.65), residues: 34 sheet: 0.56 (0.42), residues: 141 loop : -0.35 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 50 HIS 0.001 0.001 HIS L 90 PHE 0.023 0.002 PHE A 400 TYR 0.033 0.002 TYR A 453 ARG 0.005 0.001 ARG L 45 *********************** 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 87 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 LYS cc_start: 0.8786 (tttm) cc_final: 0.8551 (tttm) REVERT: H 39 GLN cc_start: 0.7022 (tm-30) cc_final: 0.6703 (tm-30) REVERT: H 80 MET cc_start: 0.4807 (mtp) cc_final: 0.4360 (mtp) REVERT: A 375 SER cc_start: 0.8958 (p) cc_final: 0.8706 (t) REVERT: A 473 TYR cc_start: 0.8259 (t80) cc_final: 0.7855 (t80) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1518 time to fit residues: 16.1087 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 : 0.358 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.190912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169512 restraints weight = 6455.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173445 restraints weight = 4292.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176420 restraints weight = 3119.426| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.8514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3405 Z= 0.210 Angle : 0.642 11.043 4622 Z= 0.339 Chirality : 0.048 0.259 498 Planarity : 0.005 0.066 596 Dihedral : 5.427 31.797 491 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % 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: -0.50 (0.42), residues: 419 helix: -3.51 (0.70), residues: 34 sheet: 0.59 (0.42), residues: 141 loop : -0.36 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 50 HIS 0.001 0.000 HIS L 90 PHE 0.011 0.002 PHE H 29 TYR 0.029 0.002 TYR A 453 ARG 0.005 0.001 ARG A 509 ********************** 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 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 91 TYR cc_start: 0.7410 (m-10) cc_final: 0.6929 (m-10) REVERT: L 103 LYS cc_start: 0.8758 (tttm) cc_final: 0.8505 (tttm) REVERT: H 39 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6790 (tm-30) REVERT: H 79 TYR cc_start: 0.7249 (m-10) cc_final: 0.6963 (m-10) REVERT: A 375 SER cc_start: 0.8846 (p) cc_final: 0.8585 (t) REVERT: A 423 TYR cc_start: 0.7362 (t80) cc_final: 0.7119 (t80) REVERT: A 473 TYR cc_start: 0.8194 (t80) cc_final: 0.7782 (t80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1353 time to fit residues: 15.0006 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 : 0.544 ------------------------------------------------------------------------------- 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: 0.0670 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 5 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.191479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169763 restraints weight = 6359.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173869 restraints weight = 4180.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176862 restraints weight = 3023.902| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.8639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3405 Z= 0.192 Angle : 0.631 10.567 4622 Z= 0.335 Chirality : 0.048 0.242 498 Planarity : 0.005 0.067 596 Dihedral : 5.287 30.884 491 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.28 % Allowed : 0.00 % 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: -0.33 (0.42), residues: 419 helix: -3.56 (0.69), residues: 35 sheet: 0.97 (0.46), residues: 119 loop : -0.26 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 36 HIS 0.001 0.001 HIS L 90 PHE 0.023 0.002 PHE A 400 TYR 0.027 0.002 TYR A 453 ARG 0.007 0.001 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.19 seconds wall clock time: 29 minutes 45.20 seconds (1785.20 seconds total)