Starting phenix.real_space_refine on Mon Feb 10 21:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm0_27522/02_2025/8dm0_27522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm0_27522/02_2025/8dm0_27522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm0_27522/02_2025/8dm0_27522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm0_27522/02_2025/8dm0_27522.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm0_27522/02_2025/8dm0_27522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm0_27522/02_2025/8dm0_27522.cif" } resolution = 3.21 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= -0.000 sd= 0.014 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 13 5.16 5 C 1582 2.51 5 N 414 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 2480 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" 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: 3.19, per 1000 atoms: 1.29 Number of scatterers: 2480 At special positions: 0 Unit cell: (68, 81, 70, 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 13 16.00 O 471 8.00 N 414 7.00 C 1582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 321.2 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.552A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.078A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.276A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.512A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.647A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.710A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.129A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 183 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: 0.50 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 786 1.34 - 1.46: 647 1.46 - 1.58: 1097 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 2547 Sorted by residual: bond pdb=" CB PRO H 14 " pdb=" CG PRO H 14 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.83e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.40e+00 ... (remaining 2542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 3318 2.25 - 4.50: 126 4.50 - 6.74: 16 6.74 - 8.99: 4 8.99 - 11.24: 2 Bond angle restraints: 3466 Sorted by residual: angle pdb=" C TYR C 505 " pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta sigma weight residual 120.68 131.92 -11.24 1.52e+00 4.33e-01 5.47e+01 angle pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 112.00 103.09 8.91 1.40e+00 5.10e-01 4.05e+01 angle pdb=" N PRO H 14 " pdb=" CA PRO H 14 " pdb=" C PRO H 14 " ideal model delta sigma weight residual 110.55 118.61 -8.06 1.63e+00 3.76e-01 2.45e+01 angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 119.56 -6.96 1.70e+00 3.46e-01 1.68e+01 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 126.99 -10.69 3.50e+00 8.16e-02 9.33e+00 ... (remaining 3461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 1304 13.80 - 27.59: 143 27.59 - 41.39: 42 41.39 - 55.18: 7 55.18 - 68.98: 1 Dihedral angle restraints: 1497 sinusoidal: 590 harmonic: 907 Sorted by residual: dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 132.19 -39.19 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA VAL C 483 " pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta harmonic sigma weight residual 180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 280 0.061 - 0.122: 77 0.122 - 0.183: 10 0.183 - 0.243: 2 0.243 - 0.304: 2 Chirality restraints: 371 Sorted by residual: chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ASN C 440 " pdb=" N ASN C 440 " pdb=" C ASN C 440 " pdb=" CB ASN C 440 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 368 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.058 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO H 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 473 " -0.013 2.00e-02 2.50e+03 1.86e-02 6.95e+00 pdb=" CG TYR C 473 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 473 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 473 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 473 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 473 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 473 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 473 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO C 521 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 703 2.81 - 3.33: 1952 3.33 - 3.86: 3972 3.86 - 4.38: 4564 4.38 - 4.90: 8063 Nonbonded interactions: 19254 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.288 3.040 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.401 3.120 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.486 3.040 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.514 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.528 3.120 ... (remaining 19249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.006 0.121 2547 Z= 0.420 Angle : 1.006 11.238 3466 Z= 0.566 Chirality : 0.060 0.304 371 Planarity : 0.009 0.083 447 Dihedral : 12.719 68.980 910 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.40), residues: 310 helix: -4.74 (0.24), residues: 26 sheet: -0.29 (0.50), residues: 96 loop : -1.12 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 109 HIS 0.007 0.002 HIS H 35 PHE 0.020 0.003 PHE C 497 TYR 0.046 0.002 TYR C 473 ARG 0.012 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: H 60 ASN cc_start: 0.9086 (t0) cc_final: 0.8884 (t0) REVERT: H 98 VAL cc_start: 0.8299 (m) cc_final: 0.8026 (t) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1769 time to fit residues: 16.3763 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3554 r_free = 0.3554 target = 0.117772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100856 restraints weight = 4581.838| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.27 r_work: 0.3176 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2547 Z= 0.194 Angle : 0.591 9.244 3466 Z= 0.299 Chirality : 0.045 0.145 371 Planarity : 0.005 0.044 447 Dihedral : 5.603 25.431 372 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.75 % Allowed : 9.74 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.41), residues: 310 helix: -3.52 (0.65), residues: 26 sheet: -0.18 (0.50), residues: 96 loop : -0.86 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE C 377 TYR 0.009 0.001 TYR C 365 ARG 0.004 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: C 417 LYS cc_start: 0.8358 (mmtp) cc_final: 0.7971 (mtpt) REVERT: H 13 GLN cc_start: 0.8375 (mp10) cc_final: 0.8169 (mp10) REVERT: H 60 ASN cc_start: 0.9236 (t0) cc_final: 0.8787 (t0) outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 0.1783 time to fit residues: 16.7944 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.5626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3533 r_free = 0.3533 target = 0.115871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099825 restraints weight = 4487.449| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.03 r_work: 0.3167 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2547 Z= 0.197 Angle : 0.586 6.793 3466 Z= 0.292 Chirality : 0.044 0.139 371 Planarity : 0.004 0.036 447 Dihedral : 4.997 20.883 372 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.62 % Allowed : 11.61 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.42), residues: 310 helix: -3.24 (0.78), residues: 27 sheet: -0.10 (0.50), residues: 96 loop : -0.76 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.001 HIS H 35 PHE 0.024 0.002 PHE C 456 TYR 0.012 0.001 TYR C 473 ARG 0.006 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.286 Fit side-chains REVERT: C 417 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8012 (mtpt) REVERT: H 13 GLN cc_start: 0.8462 (mp10) cc_final: 0.8238 (mp10) REVERT: H 19 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7557 (tpp80) REVERT: H 60 ASN cc_start: 0.9149 (t0) cc_final: 0.8726 (t0) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.1964 time to fit residues: 18.3080 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3528 r_free = 0.3528 target = 0.115461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099569 restraints weight = 4666.394| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.06 r_work: 0.3173 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2547 Z= 0.195 Angle : 0.564 5.536 3466 Z= 0.283 Chirality : 0.044 0.135 371 Planarity : 0.004 0.034 447 Dihedral : 4.786 17.597 372 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.62 % Allowed : 13.11 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.42), residues: 310 helix: -3.25 (0.82), residues: 27 sheet: -0.14 (0.51), residues: 91 loop : -0.74 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.001 0.000 HIS H 35 PHE 0.010 0.001 PHE C 377 TYR 0.010 0.001 TYR C 495 ARG 0.004 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.263 Fit side-chains REVERT: C 417 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8042 (mtpt) REVERT: H 19 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7643 (tpp80) REVERT: H 60 ASN cc_start: 0.9171 (t0) cc_final: 0.8761 (t0) REVERT: H 66 LEU cc_start: 0.8005 (mt) cc_final: 0.7759 (mm) REVERT: H 106 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8198 (mtt) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.2010 time to fit residues: 18.2073 Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3528 r_free = 0.3528 target = 0.115294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098955 restraints weight = 4679.496| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.14 r_work: 0.3142 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2547 Z= 0.210 Angle : 0.579 5.462 3466 Z= 0.288 Chirality : 0.044 0.135 371 Planarity : 0.004 0.034 447 Dihedral : 4.686 17.186 372 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.00 % Allowed : 15.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.42), residues: 310 helix: -3.17 (0.85), residues: 27 sheet: -0.20 (0.51), residues: 91 loop : -0.75 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS H 53 PHE 0.010 0.001 PHE C 377 TYR 0.010 0.001 TYR C 473 ARG 0.005 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.280 Fit side-chains REVERT: C 417 LYS cc_start: 0.8432 (mmtp) cc_final: 0.8036 (mtpt) REVERT: H 19 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7448 (tpp80) REVERT: H 60 ASN cc_start: 0.9174 (t0) cc_final: 0.8753 (t0) REVERT: H 81 GLN cc_start: 0.8573 (tp40) cc_final: 0.7768 (tp40) REVERT: H 106 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8146 (mtt) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.1950 time to fit residues: 17.0639 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.114093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097768 restraints weight = 4660.644| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.10 r_work: 0.3130 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2547 Z= 0.231 Angle : 0.587 5.518 3466 Z= 0.294 Chirality : 0.044 0.132 371 Planarity : 0.004 0.034 447 Dihedral : 4.663 17.364 372 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.37 % Allowed : 16.48 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.43), residues: 310 helix: -3.10 (0.88), residues: 26 sheet: -0.06 (0.50), residues: 96 loop : -0.79 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.001 0.001 HIS H 35 PHE 0.011 0.001 PHE H 29 TYR 0.010 0.001 TYR H 79 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.284 Fit side-chains REVERT: C 417 LYS cc_start: 0.8387 (mmtp) cc_final: 0.7971 (mtmt) REVERT: H 19 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: H 60 ASN cc_start: 0.9171 (t0) cc_final: 0.8771 (t0) REVERT: H 66 LEU cc_start: 0.8556 (mm) cc_final: 0.8187 (mt) REVERT: H 81 GLN cc_start: 0.8560 (tp40) cc_final: 0.7966 (tp40) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.1940 time to fit residues: 17.0192 Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.113955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097862 restraints weight = 4714.816| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.09 r_work: 0.3132 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2547 Z= 0.226 Angle : 0.588 6.085 3466 Z= 0.295 Chirality : 0.045 0.137 371 Planarity : 0.004 0.034 447 Dihedral : 4.632 17.142 372 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.25 % Allowed : 17.23 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.43), residues: 310 helix: -3.04 (0.90), residues: 26 sheet: -0.03 (0.50), residues: 96 loop : -0.78 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 109 HIS 0.001 0.001 HIS H 53 PHE 0.010 0.001 PHE H 29 TYR 0.010 0.001 TYR C 473 ARG 0.003 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.280 Fit side-chains REVERT: C 417 LYS cc_start: 0.8386 (mmtp) cc_final: 0.7983 (mtmt) REVERT: H 19 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7434 (tpp80) REVERT: H 60 ASN cc_start: 0.9195 (t0) cc_final: 0.8798 (t0) REVERT: H 81 GLN cc_start: 0.8548 (tp40) cc_final: 0.7758 (tp40) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.2052 time to fit residues: 17.7073 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3540 r_free = 0.3540 target = 0.116251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099842 restraints weight = 4740.164| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.16 r_work: 0.3161 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2547 Z= 0.171 Angle : 0.571 7.125 3466 Z= 0.285 Chirality : 0.044 0.129 371 Planarity : 0.003 0.034 447 Dihedral : 4.362 16.471 372 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.62 % Allowed : 17.60 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.44), residues: 310 helix: -3.09 (0.87), residues: 26 sheet: 0.21 (0.53), residues: 90 loop : -0.67 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 109 HIS 0.001 0.000 HIS H 35 PHE 0.008 0.001 PHE C 377 TYR 0.011 0.001 TYR H 79 ARG 0.003 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.294 Fit side-chains REVERT: C 417 LYS cc_start: 0.8399 (mmtp) cc_final: 0.7984 (mtmt) REVERT: H 19 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7529 (tpp80) REVERT: H 60 ASN cc_start: 0.9181 (t0) cc_final: 0.8823 (t0) REVERT: H 81 GLN cc_start: 0.8568 (tp40) cc_final: 0.7782 (tp40) outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.2121 time to fit residues: 18.8625 Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.116206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100142 restraints weight = 4588.768| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.06 r_work: 0.3169 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2547 Z= 0.190 Angle : 0.588 7.435 3466 Z= 0.295 Chirality : 0.044 0.127 371 Planarity : 0.004 0.034 447 Dihedral : 4.468 16.515 372 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.62 % Allowed : 17.60 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.44), residues: 310 helix: -3.04 (1.05), residues: 20 sheet: 0.16 (0.52), residues: 96 loop : -0.64 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.009 0.001 PHE C 377 TYR 0.008 0.001 TYR C 473 ARG 0.007 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: C 417 LYS cc_start: 0.8416 (mmtp) cc_final: 0.7977 (mtmt) REVERT: H 19 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7453 (tpp80) REVERT: H 60 ASN cc_start: 0.9183 (t0) cc_final: 0.8816 (t0) REVERT: H 81 GLN cc_start: 0.8609 (tp40) cc_final: 0.7736 (tp40) outliers start: 7 outliers final: 7 residues processed: 76 average time/residue: 0.1960 time to fit residues: 16.9051 Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.112972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096867 restraints weight = 4623.938| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.04 r_work: 0.3116 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2547 Z= 0.297 Angle : 0.633 5.642 3466 Z= 0.320 Chirality : 0.046 0.135 371 Planarity : 0.004 0.034 447 Dihedral : 4.853 17.268 372 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.62 % Allowed : 17.98 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.44), residues: 310 helix: -2.91 (0.96), residues: 26 sheet: 0.12 (0.53), residues: 96 loop : -0.80 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 36 HIS 0.001 0.001 HIS H 53 PHE 0.011 0.001 PHE C 515 TYR 0.014 0.001 TYR H 79 ARG 0.007 0.001 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.305 Fit side-chains REVERT: C 417 LYS cc_start: 0.8442 (mmtp) cc_final: 0.7989 (mtmt) REVERT: H 19 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: H 60 ASN cc_start: 0.9219 (t0) cc_final: 0.8797 (t0) REVERT: H 66 LEU cc_start: 0.8593 (mm) cc_final: 0.7875 (pp) REVERT: H 81 GLN cc_start: 0.8606 (tp40) cc_final: 0.8132 (tp40) outliers start: 7 outliers final: 7 residues processed: 74 average time/residue: 0.2117 time to fit residues: 17.7963 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.116023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099965 restraints weight = 4658.941| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.05 r_work: 0.3165 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2547 Z= 0.186 Angle : 0.586 5.480 3466 Z= 0.294 Chirality : 0.044 0.128 371 Planarity : 0.004 0.035 447 Dihedral : 4.547 16.752 372 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.62 % Allowed : 18.73 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.45), residues: 310 helix: -2.97 (0.94), residues: 26 sheet: 0.33 (0.56), residues: 90 loop : -0.67 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.008 0.001 PHE C 377 TYR 0.015 0.001 TYR H 79 ARG 0.005 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.92 seconds wall clock time: 32 minutes 55.57 seconds (1975.57 seconds total)