Starting phenix.real_space_refine on Tue Feb 11 00:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8r_27255/02_2025/8d8r_27255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8r_27255/02_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_27255/02_2025/8d8r_27255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8r_27255/02_2025/8d8r_27255.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8r_27255/02_2025/8d8r_27255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8r_27255/02_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-5592/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: 3.71, 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 410.8 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: 0.95 Time building geometry restraints manager: 0.90 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- 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 : 0.303 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: 0.1881 time to fit residues: 27.8216 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 : 0.416 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.171068 restraints weight = 6299.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175738 restraints weight = 4012.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179052 restraints weight = 2824.490| |-----------------------------------------------------------------------------| 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 : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8497 (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: 0.7542 (p0) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1474 time to fit residues: 17.7843 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.0770 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 = 0.194538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.172606 restraints weight = 6052.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.177113 restraints weight = 3884.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180328 restraints weight = 2727.596| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.4704 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= 0.193 Angle : 0.558 5.083 4622 Z= 0.310 Chirality : 0.043 0.132 498 Planarity : 0.005 0.054 596 Dihedral : 4.658 18.339 491 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 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 0.018 0.002 TRP A 353 HIS 0.002 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 96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8236 (m100) cc_final: 0.7775 (m100) REVERT: H 111 GLN cc_start: 0.7320 (pm20) cc_final: 0.7094 (pt0) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1491 time to fit residues: 17.4340 Evaluate side-chains 83 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.4980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 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 L 90 HIS H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.185585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161566 restraints weight = 6387.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165990 restraints weight = 4154.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169177 restraints weight = 2974.920| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3405 Z= 0.329 Angle : 0.720 10.877 4622 Z= 0.396 Chirality : 0.048 0.252 498 Planarity : 0.006 0.060 596 Dihedral : 5.903 32.469 491 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.06 % 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: -0.03 (0.41), residues: 419 helix: -3.57 (0.65), residues: 28 sheet: 0.25 (0.39), residues: 153 loop : 0.41 (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 0.032 0.003 PHE A 400 TYR 0.028 0.003 TYR L 32 ARG 0.011 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 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8578 (m100) cc_final: 0.8355 (m100) REVERT: H 39 GLN cc_start: 0.7403 (tm-30) cc_final: 0.6671 (tm-30) REVERT: H 50 TRP cc_start: 0.7289 (p-90) cc_final: 0.7063 (p-90) REVERT: H 68 THR cc_start: 0.6869 (m) cc_final: 0.6667 (t) REVERT: H 73 MET cc_start: 0.8424 (mmm) cc_final: 0.7796 (mmm) REVERT: H 79 TYR cc_start: 0.7285 (m-80) cc_final: 0.7030 (m-10) REVERT: H 111 GLN cc_start: 0.7693 (pm20) cc_final: 0.7458 (pt0) REVERT: A 473 TYR cc_start: 0.8483 (t80) cc_final: 0.8263 (t80) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1602 time to fit residues: 18.2822 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 : 0.375 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.0020 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.189523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166969 restraints weight = 6360.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171579 restraints weight = 4115.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174746 restraints weight = 2901.867| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3405 Z= 0.225 Angle : 0.694 17.124 4622 Z= 0.372 Chirality : 0.048 0.366 498 Planarity : 0.005 0.056 596 Dihedral : 5.399 32.207 491 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: -0.05 (0.41), residues: 419 helix: -3.41 (0.77), residues: 28 sheet: 0.42 (0.41), residues: 142 loop : 0.23 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 96 HIS 0.006 0.002 HIS L 90 PHE 0.023 0.002 PHE H 29 TYR 0.022 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 94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 TYR cc_start: 0.7354 (m-10) cc_final: 0.6539 (m-10) REVERT: H 36 TRP cc_start: 0.8303 (m100) cc_final: 0.8000 (m100) REVERT: H 50 TRP cc_start: 0.7169 (p-90) cc_final: 0.6899 (p-90) REVERT: H 68 THR cc_start: 0.6785 (m) cc_final: 0.6557 (t) REVERT: H 79 TYR cc_start: 0.7256 (m-80) cc_final: 0.6987 (m-10) REVERT: H 111 GLN cc_start: 0.7735 (pm20) cc_final: 0.7382 (pt0) REVERT: A 473 TYR cc_start: 0.8496 (t80) cc_final: 0.8203 (t80) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1478 time to fit residues: 16.9918 Evaluate side-chains 83 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.185465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162348 restraints weight = 6583.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166776 restraints weight = 4261.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169813 restraints weight = 3049.039| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3405 Z= 0.282 Angle : 0.723 15.099 4622 Z= 0.390 Chirality : 0.049 0.328 498 Planarity : 0.005 0.052 596 Dihedral : 6.109 40.409 491 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % 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: -0.37 (0.41), residues: 419 helix: -3.68 (0.66), residues: 28 sheet: 0.52 (0.42), residues: 141 loop : -0.21 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 96 HIS 0.007 0.003 HIS L 90 PHE 0.040 0.002 PHE A 400 TYR 0.029 0.003 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 : 0.357 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8625 (m100) cc_final: 0.8143 (m100) REVERT: H 50 TRP cc_start: 0.7881 (p-90) cc_final: 0.7413 (p-90) REVERT: H 111 GLN cc_start: 0.7955 (pm20) cc_final: 0.7697 (pt0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1384 time to fit residues: 16.3827 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 : 0.356 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 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 ** 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 = 0.4184 r_free = 0.4184 target = 0.184711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162382 restraints weight = 6560.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166578 restraints weight = 4324.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169465 restraints weight = 3128.157| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.8020 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= 0.314 Angle : 0.744 15.334 4622 Z= 0.404 Chirality : 0.050 0.304 498 Planarity : 0.005 0.070 596 Dihedral : 6.529 40.896 491 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % 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: -0.72 (0.42), residues: 419 helix: -3.74 (0.62), residues: 34 sheet: 0.34 (0.43), residues: 143 loop : -0.42 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 96 HIS 0.003 0.002 HIS A 519 PHE 0.016 0.002 PHE A 400 TYR 0.027 0.003 TYR H 59 ARG 0.003 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 93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8565 (m100) cc_final: 0.8115 (m100) REVERT: H 50 TRP cc_start: 0.7981 (p-90) cc_final: 0.7487 (p-90) REVERT: H 52 VAL cc_start: 0.8817 (t) cc_final: 0.8525 (t) REVERT: H 80 MET cc_start: 0.4753 (mtp) cc_final: 0.4397 (mtp) REVERT: H 111 GLN cc_start: 0.7897 (pm20) cc_final: 0.7393 (pt0) REVERT: A 351 TYR cc_start: 0.7659 (p90) cc_final: 0.7396 (p90) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1662 time to fit residues: 18.8687 Evaluate side-chains 79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 0.0070 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.0050 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4612 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.187916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165517 restraints weight = 6379.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169641 restraints weight = 4142.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172685 restraints weight = 2974.935| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3405 Z= 0.232 Angle : 0.688 12.713 4622 Z= 0.370 Chirality : 0.050 0.308 498 Planarity : 0.005 0.070 596 Dihedral : 5.975 32.796 491 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % 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: -0.68 (0.42), residues: 419 helix: -3.60 (0.69), residues: 34 sheet: 0.47 (0.43), residues: 143 loop : -0.48 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 96 HIS 0.003 0.001 HIS L 90 PHE 0.013 0.002 PHE H 27 TYR 0.028 0.002 TYR A 453 ARG 0.005 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 88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 20 VAL cc_start: 0.8685 (t) cc_final: 0.8435 (t) REVERT: H 36 TRP cc_start: 0.8425 (m100) cc_final: 0.8204 (m100) REVERT: H 50 TRP cc_start: 0.7867 (p-90) cc_final: 0.7278 (p-90) REVERT: H 52 VAL cc_start: 0.8835 (t) cc_final: 0.8552 (t) REVERT: H 79 TYR cc_start: 0.7258 (m-10) cc_final: 0.6887 (m-10) REVERT: H 111 GLN cc_start: 0.7883 (pm20) cc_final: 0.7288 (pt0) REVERT: A 403 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7767 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1608 time to fit residues: 17.1298 Evaluate side-chains 77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 0.0170 chunk 39 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 chunk 5 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 overall best weight: 0.1356 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.193313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.171967 restraints weight = 6375.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176102 restraints weight = 4112.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179133 restraints weight = 2917.675| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.8258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3405 Z= 0.160 Angle : 0.626 11.089 4622 Z= 0.333 Chirality : 0.047 0.254 498 Planarity : 0.005 0.070 596 Dihedral : 5.078 26.639 491 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -0.48 (0.42), residues: 419 helix: -3.50 (0.73), residues: 35 sheet: 0.83 (0.45), residues: 131 loop : -0.43 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 96 HIS 0.003 0.001 HIS L 90 PHE 0.019 0.002 PHE A 400 TYR 0.023 0.002 TYR A 495 ARG 0.004 0.000 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 89 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 50 TRP cc_start: 0.7711 (p-90) cc_final: 0.7359 (p-90) REVERT: H 52 VAL cc_start: 0.8761 (t) cc_final: 0.8455 (t) REVERT: H 79 TYR cc_start: 0.7158 (m-10) cc_final: 0.6915 (m-10) REVERT: H 80 MET cc_start: 0.4446 (mtp) cc_final: 0.3881 (mtp) REVERT: H 111 GLN cc_start: 0.7741 (pm20) cc_final: 0.6781 (pt0) REVERT: A 403 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7693 (mtt-85) REVERT: A 516 GLU cc_start: 0.6103 (tt0) cc_final: 0.5756 (tt0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1607 time to fit residues: 17.3595 Evaluate side-chains 79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.191656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169970 restraints weight = 6318.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174180 restraints weight = 4121.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.177264 restraints weight = 2953.800| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.8466 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= 0.206 Angle : 0.651 10.996 4622 Z= 0.346 Chirality : 0.049 0.251 498 Planarity : 0.005 0.068 596 Dihedral : 5.301 28.952 491 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.61 (0.42), residues: 419 helix: -3.41 (0.74), residues: 34 sheet: 0.72 (0.45), residues: 131 loop : -0.56 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP H 36 HIS 0.003 0.001 HIS L 90 PHE 0.013 0.002 PHE H 29 TYR 0.022 0.002 TYR A 495 ARG 0.006 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 83 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.7208 (m-10) cc_final: 0.6924 (m-10) REVERT: H 111 GLN cc_start: 0.7809 (pm20) cc_final: 0.7116 (pt0) REVERT: A 403 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7914 (mtp85) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1644 time to fit residues: 16.5359 Evaluate side-chains 79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.2980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.0170 chunk 5 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.193710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172701 restraints weight = 6270.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176707 restraints weight = 4172.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179503 restraints weight = 3000.570| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.8557 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= 0.178 Angle : 0.627 10.403 4622 Z= 0.334 Chirality : 0.049 0.255 498 Planarity : 0.005 0.069 596 Dihedral : 5.175 29.387 491 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.38 (0.73), residues: 34 sheet: 0.97 (0.47), residues: 121 loop : -0.52 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 50 HIS 0.003 0.001 HIS L 90 PHE 0.014 0.002 PHE H 29 TYR 0.022 0.001 TYR A 495 ARG 0.005 0.000 ARG L 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.15 seconds wall clock time: 29 minutes 10.74 seconds (1750.74 seconds total)