Starting phenix.real_space_refine on Wed Mar 5 17:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5f_24188/03_2025/7n5f_24188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5f_24188/03_2025/7n5f_24188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5f_24188/03_2025/7n5f_24188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5f_24188/03_2025/7n5f_24188.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5f_24188/03_2025/7n5f_24188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5f_24188/03_2025/7n5f_24188.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 12 5.16 5 C 1996 2.51 5 N 503 2.21 5 O 526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3037 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.91 Number of scatterers: 3037 At special positions: 0 Unit cell: (56.65, 90.64, 141.11, 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 12 16.00 O 526 8.00 N 503 7.00 C 1996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 346.0 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 64.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.854A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 259 through 283 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 504 through 552 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 661 through 678 Processing helix chain 'A' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.273A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.531A pdb=" N LYS A 699 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 694 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 701 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 707 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 686 " --> pdb=" O ASN A 707 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 654 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: 0.80 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 824 1.44 - 1.56: 1667 1.56 - 1.69: 16 1.69 - 1.82: 21 Bond restraints: 3094 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.39e+01 bond pdb=" CB ILE A 285 " pdb=" CG1 ILE A 285 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" NE1 TRP A 273 " pdb=" CE2 TRP A 273 " ideal model delta sigma weight residual 1.370 1.315 0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" CB LEU A 258 " pdb=" CG LEU A 258 " ideal model delta sigma weight residual 1.530 1.628 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CB TYR A 629 " pdb=" CG TYR A 629 " ideal model delta sigma weight residual 1.512 1.406 0.106 2.20e-02 2.07e+03 2.34e+01 ... (remaining 3089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 3277 1.65 - 3.31: 716 3.31 - 4.96: 159 4.96 - 6.61: 32 6.61 - 8.27: 6 Bond angle restraints: 4190 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.07 -8.27 1.00e+00 1.00e+00 6.83e+01 angle pdb=" C LEU A 743 " pdb=" N PRO A 744 " pdb=" CA PRO A 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C HIS A 592 " pdb=" N PRO A 593 " pdb=" CA PRO A 593 " ideal model delta sigma weight residual 119.56 125.29 -5.73 1.01e+00 9.80e-01 3.22e+01 angle pdb=" C SER A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 120.98 126.89 -5.91 1.07e+00 8.73e-01 3.05e+01 angle pdb=" C TYR A 629 " pdb=" N PRO A 630 " pdb=" CA PRO A 630 " ideal model delta sigma weight residual 119.76 125.32 -5.56 1.03e+00 9.43e-01 2.91e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1782 17.70 - 35.40: 36 35.40 - 53.09: 8 53.09 - 70.79: 2 70.79 - 88.49: 3 Dihedral angle restraints: 1831 sinusoidal: 699 harmonic: 1132 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.65 8.15 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.49 88.49 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 1828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 408 0.108 - 0.216: 84 0.216 - 0.323: 12 0.323 - 0.431: 0 0.431 - 0.539: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA PHE A 335 " pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CB PHE A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 503 not shown) Planarity restraints: 511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 697 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C VAL A 697 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL A 697 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C SER A 329 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 508 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1532 2.95 - 3.44: 3149 3.44 - 3.93: 4806 3.93 - 4.41: 5610 4.41 - 4.90: 8455 Nonbonded interactions: 23552 Sorted by model distance: nonbonded pdb=" N ASN A 711 " pdb=" O ASN A 711 " model vdw 2.468 2.496 nonbonded pdb=" NZ LYS A 730 " pdb=" OE2 GLU A 734 " model vdw 2.473 3.120 nonbonded pdb=" N VAL A 697 " pdb=" N ASN A 698 " model vdw 2.491 2.560 nonbonded pdb=" NZ LYS A 579 " pdb=" OE2 GLU A 583 " model vdw 2.506 3.120 nonbonded pdb=" N THR A 295 " pdb=" N ARG A 296 " model vdw 2.536 2.560 ... (remaining 23547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.060 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: 0.020 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.023 0.124 3094 Z= 1.447 Angle : 1.502 8.265 4190 Z= 1.032 Chirality : 0.097 0.539 506 Planarity : 0.008 0.037 511 Dihedral : 9.991 88.488 1085 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.68 (0.40), residues: 374 helix: 1.43 (0.29), residues: 242 sheet: 0.14 (0.80), residues: 38 loop : 1.02 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP A 622 HIS 0.009 0.003 HIS A 331 PHE 0.059 0.006 PHE A 335 TYR 0.026 0.006 TYR A 675 ARG 0.007 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.320 Fit side-chains REVERT: A 350 GLN cc_start: 0.7950 (mt0) cc_final: 0.7715 (mt0) REVERT: A 548 TRP cc_start: 0.8678 (t60) cc_final: 0.8248 (t60) REVERT: A 591 MET cc_start: 0.7817 (mtp) cc_final: 0.7553 (mtp) REVERT: A 624 LYS cc_start: 0.8810 (mmtp) cc_final: 0.7292 (tmmt) REVERT: A 655 SER cc_start: 0.8107 (p) cc_final: 0.7870 (m) REVERT: A 675 TYR cc_start: 0.8227 (t80) cc_final: 0.7937 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.9135 time to fit residues: 143.0180 Evaluate side-chains 133 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.154276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137704 restraints weight = 4641.303| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.02 r_work: 0.3799 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3094 Z= 0.230 Angle : 0.552 6.158 4190 Z= 0.310 Chirality : 0.042 0.150 506 Planarity : 0.003 0.028 511 Dihedral : 5.847 46.720 411 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.13 % Allowed : 18.41 % Favored : 77.46 % 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: 3.33 (0.45), residues: 374 helix: 2.92 (0.32), residues: 232 sheet: 0.61 (0.72), residues: 44 loop : 1.32 (0.80), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 507 HIS 0.008 0.002 HIS A 331 PHE 0.011 0.002 PHE A 733 TYR 0.008 0.001 TYR A 628 ARG 0.003 0.001 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.365 Fit side-chains REVERT: A 261 THR cc_start: 0.7248 (m) cc_final: 0.7047 (p) REVERT: A 576 ASN cc_start: 0.7588 (t0) cc_final: 0.7309 (t0) REVERT: A 624 LYS cc_start: 0.8806 (mmtp) cc_final: 0.6736 (tmmt) REVERT: A 626 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.4301 (mptp) REVERT: A 655 SER cc_start: 0.8653 (p) cc_final: 0.8338 (m) REVERT: A 728 GLU cc_start: 0.7343 (tp30) cc_final: 0.7103 (tp30) REVERT: A 737 ASP cc_start: 0.7759 (t0) cc_final: 0.7491 (t0) outliers start: 13 outliers final: 4 residues processed: 132 average time/residue: 0.9058 time to fit residues: 123.3410 Evaluate side-chains 129 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 632 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.153971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.136913 restraints weight = 4568.905| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.99 r_work: 0.3793 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3094 Z= 0.194 Angle : 0.479 6.187 4190 Z= 0.272 Chirality : 0.042 0.155 506 Planarity : 0.003 0.031 511 Dihedral : 5.519 45.033 411 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.35 % Allowed : 22.86 % Favored : 70.79 % 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: 3.32 (0.45), residues: 374 helix: 2.96 (0.32), residues: 233 sheet: 0.83 (0.75), residues: 44 loop : 1.01 (0.78), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.005 0.002 HIS A 592 PHE 0.015 0.001 PHE A 260 TYR 0.010 0.001 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 271 PHE cc_start: 0.8255 (t80) cc_final: 0.8045 (t80) REVERT: A 576 ASN cc_start: 0.7628 (t0) cc_final: 0.7350 (t0) REVERT: A 624 LYS cc_start: 0.8831 (mmtp) cc_final: 0.6777 (tmmt) REVERT: A 626 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.4263 (mptp) REVERT: A 645 SER cc_start: 0.8498 (m) cc_final: 0.8283 (p) REVERT: A 648 GLN cc_start: 0.8131 (mt0) cc_final: 0.7923 (mt0) REVERT: A 655 SER cc_start: 0.8639 (p) cc_final: 0.8347 (m) REVERT: A 699 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8109 (ttmt) REVERT: A 737 ASP cc_start: 0.7846 (t0) cc_final: 0.7571 (t0) outliers start: 20 outliers final: 5 residues processed: 126 average time/residue: 0.9989 time to fit residues: 129.6114 Evaluate side-chains 123 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 = 0.4135 r_free = 0.4135 target = 0.153986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136606 restraints weight = 4625.352| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.03 r_work: 0.3789 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3094 Z= 0.183 Angle : 0.465 5.997 4190 Z= 0.261 Chirality : 0.042 0.150 506 Planarity : 0.003 0.030 511 Dihedral : 5.391 43.942 411 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.08 % Allowed : 25.08 % Favored : 69.84 % 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: 3.37 (0.45), residues: 374 helix: 3.10 (0.33), residues: 233 sheet: 0.79 (0.76), residues: 44 loop : 0.76 (0.76), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.004 0.002 HIS A 592 PHE 0.009 0.001 PHE A 330 TYR 0.020 0.002 TYR A 675 ARG 0.003 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 535 LEU cc_start: 0.8658 (tm) cc_final: 0.8450 (tp) REVERT: A 573 ILE cc_start: 0.8295 (mp) cc_final: 0.8095 (mp) REVERT: A 576 ASN cc_start: 0.7586 (t0) cc_final: 0.7208 (t0) REVERT: A 624 LYS cc_start: 0.8831 (mmtp) cc_final: 0.6819 (tmmt) REVERT: A 626 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.4215 (mptp) REVERT: A 655 SER cc_start: 0.8672 (p) cc_final: 0.8364 (m) REVERT: A 671 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: A 737 ASP cc_start: 0.7965 (t0) cc_final: 0.7613 (t0) outliers start: 16 outliers final: 6 residues processed: 123 average time/residue: 1.0029 time to fit residues: 126.9493 Evaluate side-chains 124 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 626 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 = 0.4136 r_free = 0.4136 target = 0.154073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136559 restraints weight = 4613.374| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.00 r_work: 0.3790 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3094 Z= 0.181 Angle : 0.455 5.750 4190 Z= 0.257 Chirality : 0.041 0.166 506 Planarity : 0.003 0.030 511 Dihedral : 5.638 49.999 411 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.71 % Allowed : 25.40 % Favored : 68.89 % 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: 3.35 (0.45), residues: 374 helix: 3.17 (0.33), residues: 233 sheet: 0.74 (0.76), residues: 44 loop : 0.55 (0.75), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.018 0.002 PHE A 271 TYR 0.019 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 316 TRP cc_start: 0.8403 (OUTLIER) cc_final: 0.6922 (t60) REVERT: A 522 LEU cc_start: 0.8780 (mm) cc_final: 0.8569 (mp) REVERT: A 573 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 576 ASN cc_start: 0.7615 (t0) cc_final: 0.7375 (t0) REVERT: A 581 ILE cc_start: 0.7966 (mm) cc_final: 0.7706 (mp) REVERT: A 624 LYS cc_start: 0.8829 (mmtp) cc_final: 0.6819 (tmmt) REVERT: A 626 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.4136 (mptp) REVERT: A 655 SER cc_start: 0.8661 (p) cc_final: 0.8381 (m) REVERT: A 737 ASP cc_start: 0.7998 (t0) cc_final: 0.7613 (t0) outliers start: 18 outliers final: 9 residues processed: 126 average time/residue: 0.9569 time to fit residues: 124.2358 Evaluate side-chains 132 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 = 0.4138 r_free = 0.4138 target = 0.154212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136655 restraints weight = 4692.172| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.04 r_work: 0.3788 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3094 Z= 0.174 Angle : 0.471 7.025 4190 Z= 0.258 Chirality : 0.041 0.168 506 Planarity : 0.003 0.030 511 Dihedral : 5.466 51.744 411 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 6.03 % Allowed : 26.35 % Favored : 67.62 % 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: 3.31 (0.46), residues: 374 helix: 3.12 (0.33), residues: 233 sheet: 0.78 (0.77), residues: 44 loop : 0.53 (0.76), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.017 0.001 PHE A 271 TYR 0.021 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 316 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.6879 (t60) REVERT: A 535 LEU cc_start: 0.8695 (tm) cc_final: 0.8414 (tp) REVERT: A 576 ASN cc_start: 0.7627 (t0) cc_final: 0.7405 (t0) REVERT: A 581 ILE cc_start: 0.7942 (mm) cc_final: 0.7664 (mp) REVERT: A 582 PHE cc_start: 0.8003 (t80) cc_final: 0.7560 (t80) REVERT: A 610 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: A 624 LYS cc_start: 0.8811 (mmtp) cc_final: 0.6820 (tmmt) REVERT: A 626 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.4128 (mptp) REVERT: A 655 SER cc_start: 0.8664 (p) cc_final: 0.8380 (m) REVERT: A 678 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7793 (mm-40) REVERT: A 737 ASP cc_start: 0.7970 (t0) cc_final: 0.7582 (t0) outliers start: 19 outliers final: 6 residues processed: 126 average time/residue: 0.9554 time to fit residues: 124.0747 Evaluate side-chains 128 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.153945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136548 restraints weight = 4624.486| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.01 r_work: 0.3787 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3094 Z= 0.195 Angle : 0.473 6.636 4190 Z= 0.263 Chirality : 0.042 0.171 506 Planarity : 0.003 0.030 511 Dihedral : 5.484 57.445 411 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.40 % Allowed : 26.67 % Favored : 67.94 % 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: 3.23 (0.45), residues: 374 helix: 3.07 (0.33), residues: 233 sheet: 0.84 (0.78), residues: 44 loop : 0.43 (0.75), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.015 0.001 PHE A 271 TYR 0.016 0.002 TYR A 675 ARG 0.003 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 316 TRP cc_start: 0.8415 (OUTLIER) cc_final: 0.6860 (t60) REVERT: A 576 ASN cc_start: 0.7600 (t0) cc_final: 0.7166 (t0) REVERT: A 581 ILE cc_start: 0.7935 (mm) cc_final: 0.7664 (mp) REVERT: A 610 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: A 624 LYS cc_start: 0.8815 (mmtp) cc_final: 0.6826 (tmmt) REVERT: A 626 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.4136 (mptp) REVERT: A 633 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8209 (mp) REVERT: A 655 SER cc_start: 0.8670 (p) cc_final: 0.8392 (m) REVERT: A 730 LYS cc_start: 0.8367 (tttm) cc_final: 0.8090 (tttm) REVERT: A 737 ASP cc_start: 0.8001 (t0) cc_final: 0.7592 (t0) outliers start: 17 outliers final: 8 residues processed: 124 average time/residue: 0.9759 time to fit residues: 124.4776 Evaluate side-chains 134 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.153902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136681 restraints weight = 4579.968| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.02 r_work: 0.3789 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3094 Z= 0.204 Angle : 0.494 7.540 4190 Z= 0.271 Chirality : 0.042 0.179 506 Planarity : 0.003 0.029 511 Dihedral : 5.350 55.470 411 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.08 % Allowed : 26.67 % Favored : 68.25 % 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: 3.13 (0.46), residues: 374 helix: 3.01 (0.33), residues: 234 sheet: 0.79 (0.79), residues: 44 loop : 0.31 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.014 0.001 PHE A 271 TYR 0.026 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.328 Fit side-chains REVERT: A 272 ILE cc_start: 0.8515 (mm) cc_final: 0.8235 (mp) REVERT: A 316 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.6839 (t60) REVERT: A 535 LEU cc_start: 0.8704 (tm) cc_final: 0.8416 (tp) REVERT: A 581 ILE cc_start: 0.7933 (mm) cc_final: 0.7674 (mp) REVERT: A 582 PHE cc_start: 0.8003 (t80) cc_final: 0.7607 (t80) REVERT: A 610 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: A 624 LYS cc_start: 0.8816 (mmtp) cc_final: 0.6863 (tmmt) REVERT: A 626 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.3909 (mptp) REVERT: A 655 SER cc_start: 0.8652 (p) cc_final: 0.8395 (m) REVERT: A 695 GLU cc_start: 0.7662 (tt0) cc_final: 0.7448 (tt0) REVERT: A 730 LYS cc_start: 0.8340 (tttm) cc_final: 0.8052 (tttm) REVERT: A 737 ASP cc_start: 0.8022 (t0) cc_final: 0.7607 (t0) outliers start: 16 outliers final: 9 residues processed: 127 average time/residue: 1.0366 time to fit residues: 135.4182 Evaluate side-chains 133 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 688 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.155006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137905 restraints weight = 4623.376| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.04 r_work: 0.3804 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3094 Z= 0.147 Angle : 0.462 7.226 4190 Z= 0.256 Chirality : 0.041 0.172 506 Planarity : 0.003 0.028 511 Dihedral : 5.087 53.014 411 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.13 % Allowed : 27.94 % Favored : 67.94 % 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: 3.02 (0.46), residues: 374 helix: 2.94 (0.33), residues: 240 sheet: 0.67 (0.81), residues: 42 loop : 0.06 (0.74), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.005 0.001 HIS A 592 PHE 0.018 0.001 PHE A 330 TYR 0.026 0.002 TYR A 675 ARG 0.002 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.330 Fit side-chains REVERT: A 272 ILE cc_start: 0.8501 (mm) cc_final: 0.8225 (mp) REVERT: A 316 TRP cc_start: 0.8400 (OUTLIER) cc_final: 0.6765 (t60) REVERT: A 581 ILE cc_start: 0.7871 (mm) cc_final: 0.7591 (mp) REVERT: A 582 PHE cc_start: 0.7979 (t80) cc_final: 0.7553 (t80) REVERT: A 610 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: A 624 LYS cc_start: 0.8795 (mmtp) cc_final: 0.6948 (tmmt) REVERT: A 633 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 655 SER cc_start: 0.8670 (p) cc_final: 0.8402 (m) REVERT: A 695 GLU cc_start: 0.7636 (tt0) cc_final: 0.7424 (tt0) REVERT: A 730 LYS cc_start: 0.8330 (tttm) cc_final: 0.8066 (tttm) REVERT: A 737 ASP cc_start: 0.7987 (t0) cc_final: 0.7570 (t0) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.9967 time to fit residues: 127.2031 Evaluate side-chains 128 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 648 GLN A 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.154418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137226 restraints weight = 4475.528| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.00 r_work: 0.3797 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3094 Z= 0.197 Angle : 0.497 7.992 4190 Z= 0.273 Chirality : 0.042 0.182 506 Planarity : 0.003 0.030 511 Dihedral : 4.890 46.896 411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.17 % Allowed : 29.52 % Favored : 67.30 % 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: 3.19 (0.46), residues: 374 helix: 3.07 (0.33), residues: 234 sheet: 0.82 (0.79), residues: 44 loop : 0.27 (0.76), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 683 HIS 0.004 0.001 HIS A 592 PHE 0.013 0.001 PHE A 271 TYR 0.027 0.002 TYR A 675 ARG 0.005 0.000 ARG A 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.353 Fit side-chains REVERT: A 272 ILE cc_start: 0.8518 (mm) cc_final: 0.8247 (mp) REVERT: A 316 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.6824 (t60) REVERT: A 535 LEU cc_start: 0.8672 (tm) cc_final: 0.8370 (tp) REVERT: A 582 PHE cc_start: 0.7989 (t80) cc_final: 0.7698 (t80) REVERT: A 610 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: A 624 LYS cc_start: 0.8802 (mmtp) cc_final: 0.6947 (tmmt) REVERT: A 633 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 655 SER cc_start: 0.8663 (p) cc_final: 0.8421 (m) REVERT: A 695 GLU cc_start: 0.7646 (tt0) cc_final: 0.7438 (tt0) REVERT: A 730 LYS cc_start: 0.8316 (tttm) cc_final: 0.8019 (tttm) REVERT: A 737 ASP cc_start: 0.8012 (t0) cc_final: 0.7578 (t0) outliers start: 10 outliers final: 3 residues processed: 125 average time/residue: 0.9617 time to fit residues: 123.7663 Evaluate side-chains 128 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.137132 restraints weight = 4559.550| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.02 r_work: 0.3794 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3094 Z= 0.202 Angle : 0.498 7.898 4190 Z= 0.273 Chirality : 0.042 0.177 506 Planarity : 0.003 0.029 511 Dihedral : 4.698 40.067 411 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.54 % Allowed : 30.16 % Favored : 67.30 % 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: 3.09 (0.46), residues: 374 helix: 3.04 (0.33), residues: 234 sheet: 0.80 (0.79), residues: 44 loop : 0.09 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 683 HIS 0.005 0.001 HIS A 592 PHE 0.024 0.002 PHE A 330 TYR 0.026 0.002 TYR A 675 ARG 0.005 0.000 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.29 seconds wall clock time: 66 minutes 3.98 seconds (3963.98 seconds total)