Starting phenix.real_space_refine on Mon Sep 23 13:39:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/09_2024/7n5f_24188.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/09_2024/7n5f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/09_2024/7n5f_24188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/09_2024/7n5f_24188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/09_2024/7n5f_24188.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/09_2024/7n5f_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-5461/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: 2.67, per 1000 atoms: 0.88 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: 0.71 Conformation dependent library (CDL) restraints added in 353.2 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: 0.35 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: 0.83 Time building geometry restraints manager: 0.85 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: 0.860 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.050 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.333 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: 0.8889 time to fit residues: 139.2115 Evaluate side-chains 133 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.351 Fit side-chains REVERT: A 261 THR cc_start: 0.7069 (m) cc_final: 0.6796 (p) REVERT: A 300 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7825 (mp0) REVERT: A 319 LYS cc_start: 0.7890 (tmmt) cc_final: 0.7685 (ttpt) REVERT: A 350 GLN cc_start: 0.7808 (mt0) cc_final: 0.7534 (mt0) REVERT: A 624 LYS cc_start: 0.8713 (mmtp) cc_final: 0.7111 (tmmt) REVERT: A 626 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.4433 (mptp) REVERT: A 737 ASP cc_start: 0.7511 (t0) cc_final: 0.7300 (t0) outliers start: 13 outliers final: 4 residues processed: 132 average time/residue: 0.8626 time to fit residues: 117.6041 Evaluate side-chains 129 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 28 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3748 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= 0.178 Angle : 0.474 6.127 4190 Z= 0.266 Chirality : 0.042 0.146 506 Planarity : 0.003 0.030 511 Dihedral : 5.482 45.809 411 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.03 % Allowed : 23.49 % Favored : 70.48 % 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: 3.34 (0.45), residues: 374 helix: 2.97 (0.32), residues: 233 sheet: 0.82 (0.75), residues: 44 loop : 1.05 (0.78), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.004 0.002 HIS A 592 PHE 0.015 0.001 PHE A 260 TYR 0.011 0.001 TYR A 675 ARG 0.002 0.000 ARG A 671 *********************** 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 140 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.342 Fit side-chains REVERT: A 271 PHE cc_start: 0.7890 (t80) cc_final: 0.7618 (t80) REVERT: A 350 GLN cc_start: 0.7992 (mt0) cc_final: 0.7696 (mt0) REVERT: A 624 LYS cc_start: 0.8708 (mmtp) cc_final: 0.7135 (tmmt) REVERT: A 626 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.4328 (mptp) REVERT: A 737 ASP cc_start: 0.7615 (t0) cc_final: 0.7395 (t0) outliers start: 19 outliers final: 6 residues processed: 127 average time/residue: 0.9408 time to fit residues: 123.1190 Evaluate side-chains 125 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 541 ILE 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: 0.9980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4130 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= 0.209 Angle : 0.489 6.008 4190 Z= 0.271 Chirality : 0.042 0.151 506 Planarity : 0.003 0.031 511 Dihedral : 5.441 43.301 411 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.40 % Allowed : 25.08 % Favored : 69.52 % 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: 3.32 (0.45), residues: 374 helix: 3.07 (0.33), residues: 233 sheet: 0.75 (0.76), residues: 44 loop : 0.75 (0.76), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.006 0.002 HIS A 592 PHE 0.010 0.002 PHE A 301 TYR 0.018 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 138 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.353 Fit side-chains REVERT: A 271 PHE cc_start: 0.7886 (t80) cc_final: 0.7653 (t80) REVERT: A 350 GLN cc_start: 0.7960 (mt0) cc_final: 0.7674 (mt0) REVERT: A 535 LEU cc_start: 0.8800 (tm) cc_final: 0.8577 (tp) REVERT: A 576 ASN cc_start: 0.6988 (t0) cc_final: 0.6597 (t0) REVERT: A 624 LYS cc_start: 0.8707 (mmtp) cc_final: 0.7161 (tmmt) REVERT: A 626 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.4348 (mptp) REVERT: A 737 ASP cc_start: 0.7676 (t0) cc_final: 0.7419 (t0) outliers start: 17 outliers final: 6 residues processed: 126 average time/residue: 0.9449 time to fit residues: 122.7694 Evaluate side-chains 128 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 626 LYS Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3094 Z= 0.202 Angle : 0.465 5.167 4190 Z= 0.262 Chirality : 0.041 0.164 506 Planarity : 0.003 0.030 511 Dihedral : 5.732 52.799 411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.08 % Allowed : 26.98 % 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: 3.18 (0.45), residues: 374 helix: 3.01 (0.33), residues: 233 sheet: 0.74 (0.76), residues: 44 loop : 0.51 (0.75), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.006 0.001 HIS A 592 PHE 0.015 0.001 PHE A 260 TYR 0.022 0.002 TYR A 675 ARG 0.003 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 142 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.329 Fit side-chains REVERT: A 350 GLN cc_start: 0.7965 (mt0) cc_final: 0.7685 (mt0) REVERT: A 576 ASN cc_start: 0.7082 (t0) cc_final: 0.6706 (t0) REVERT: A 582 PHE cc_start: 0.7900 (t80) cc_final: 0.7554 (t80) REVERT: A 624 LYS cc_start: 0.8700 (mmtp) cc_final: 0.7154 (tmmt) REVERT: A 626 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.4323 (mptp) REVERT: A 737 ASP cc_start: 0.7697 (t0) cc_final: 0.7463 (t0) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 0.8968 time to fit residues: 119.2533 Evaluate side-chains 132 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 541 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 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** A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3094 Z= 0.191 Angle : 0.482 6.687 4190 Z= 0.264 Chirality : 0.041 0.170 506 Planarity : 0.003 0.029 511 Dihedral : 5.395 50.605 411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 6.03 % Allowed : 26.67 % 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: 3.17 (0.45), residues: 374 helix: 3.00 (0.33), residues: 233 sheet: 0.75 (0.76), residues: 44 loop : 0.51 (0.75), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.006 0.001 HIS A 592 PHE 0.017 0.001 PHE A 330 TYR 0.024 0.002 TYR A 675 ARG 0.003 0.000 ARG A 671 *********************** 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 143 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.357 Fit side-chains REVERT: A 350 GLN cc_start: 0.7960 (mt0) cc_final: 0.7681 (mt0) REVERT: A 535 LEU cc_start: 0.8797 (tm) cc_final: 0.8554 (tp) REVERT: A 582 PHE cc_start: 0.7866 (t80) cc_final: 0.7497 (t80) REVERT: A 624 LYS cc_start: 0.8699 (mmtp) cc_final: 0.7163 (tmmt) REVERT: A 626 LYS cc_start: 0.5797 (OUTLIER) cc_final: 0.4267 (mptp) REVERT: A 737 ASP cc_start: 0.7721 (t0) cc_final: 0.7458 (t0) outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 0.8832 time to fit residues: 116.5708 Evaluate side-chains 129 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 526 LYS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3094 Z= 0.166 Angle : 0.466 6.181 4190 Z= 0.258 Chirality : 0.041 0.166 506 Planarity : 0.002 0.028 511 Dihedral : 5.429 57.910 411 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.71 % Allowed : 26.67 % 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: 2.95 (0.45), residues: 374 helix: 2.82 (0.33), residues: 240 sheet: 0.66 (0.79), residues: 42 loop : 0.24 (0.75), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.015 0.001 PHE A 260 TYR 0.022 0.002 TYR A 675 ARG 0.001 0.000 ARG A 296 *********************** 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 136 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.380 Fit side-chains REVERT: A 350 GLN cc_start: 0.7958 (mt0) cc_final: 0.7684 (mt0) REVERT: A 535 LEU cc_start: 0.8786 (tm) cc_final: 0.8566 (tp) REVERT: A 624 LYS cc_start: 0.8695 (mmtp) cc_final: 0.7248 (tmmt) REVERT: A 633 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7637 (mp) REVERT: A 737 ASP cc_start: 0.7723 (t0) cc_final: 0.7453 (t0) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 0.9544 time to fit residues: 121.7941 Evaluate side-chains 129 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 526 LYS Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 583 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 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 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 688 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3094 Z= 0.186 Angle : 0.476 5.900 4190 Z= 0.264 Chirality : 0.042 0.177 506 Planarity : 0.003 0.029 511 Dihedral : 5.339 59.359 411 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 : 4.44 % Allowed : 27.94 % 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: 2.88 (0.46), residues: 374 helix: 2.77 (0.33), residues: 240 sheet: 0.67 (0.80), residues: 42 loop : 0.19 (0.75), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 316 HIS 0.005 0.001 HIS A 592 PHE 0.008 0.001 PHE A 330 TYR 0.026 0.002 TYR A 675 ARG 0.001 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 137 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.340 Fit side-chains REVERT: A 350 GLN cc_start: 0.7967 (mt0) cc_final: 0.7693 (mt0) REVERT: A 582 PHE cc_start: 0.7862 (t80) cc_final: 0.7545 (t80) REVERT: A 624 LYS cc_start: 0.8730 (mmtp) cc_final: 0.7254 (tmmt) REVERT: A 633 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 737 ASP cc_start: 0.7717 (t0) cc_final: 0.7442 (t0) outliers start: 14 outliers final: 7 residues processed: 126 average time/residue: 0.9177 time to fit residues: 119.1123 Evaluate side-chains 130 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 566 GLN Chi-restraints excluded: chain A residue 583 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 689 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4764 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= 0.219 Angle : 0.500 7.542 4190 Z= 0.274 Chirality : 0.042 0.178 506 Planarity : 0.003 0.029 511 Dihedral : 5.036 48.050 411 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.13 % Allowed : 28.57 % 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: 3.01 (0.46), residues: 374 helix: 2.91 (0.33), residues: 234 sheet: 0.79 (0.78), residues: 44 loop : 0.23 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 316 HIS 0.005 0.001 HIS A 592 PHE 0.027 0.001 PHE A 330 TYR 0.027 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** 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 136 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.300 Fit side-chains REVERT: A 350 GLN cc_start: 0.7962 (mt0) cc_final: 0.7686 (mt0) REVERT: A 535 LEU cc_start: 0.8767 (tm) cc_final: 0.8483 (tp) REVERT: A 582 PHE cc_start: 0.7842 (t80) cc_final: 0.7615 (t80) REVERT: A 624 LYS cc_start: 0.8714 (mmtp) cc_final: 0.7180 (tmmt) REVERT: A 626 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.4293 (mptp) REVERT: A 633 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 737 ASP cc_start: 0.7746 (t0) cc_final: 0.7490 (t0) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.9454 time to fit residues: 122.7382 Evaluate side-chains 131 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 566 GLN Chi-restraints excluded: chain A residue 583 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3094 Z= 0.191 Angle : 0.511 7.366 4190 Z= 0.276 Chirality : 0.042 0.179 506 Planarity : 0.003 0.038 511 Dihedral : 4.872 45.988 411 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 2.96 (0.46), residues: 374 helix: 2.87 (0.33), residues: 234 sheet: 0.85 (0.79), residues: 44 loop : 0.19 (0.76), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 316 HIS 0.003 0.001 HIS A 592 PHE 0.014 0.001 PHE A 330 TYR 0.027 0.002 TYR A 675 ARG 0.011 0.001 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 fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.342 Fit side-chains REVERT: A 350 GLN cc_start: 0.7960 (mt0) cc_final: 0.7681 (mt0) REVERT: A 582 PHE cc_start: 0.7817 (t80) cc_final: 0.7610 (t80) REVERT: A 624 LYS cc_start: 0.8706 (mmtp) cc_final: 0.7236 (tmmt) REVERT: A 626 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.4098 (mptp) REVERT: A 633 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7660 (mp) REVERT: A 737 ASP cc_start: 0.7746 (t0) cc_final: 0.7464 (t0) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.9616 time to fit residues: 122.7525 Evaluate side-chains 129 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 532 LEU Chi-restraints excluded: chain A residue 583 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 650 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.0020 chunk 0 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.155215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138160 restraints weight = 4549.492| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.04 r_work: 0.3806 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4963 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= 0.178 Angle : 0.504 8.366 4190 Z= 0.271 Chirality : 0.042 0.178 506 Planarity : 0.003 0.049 511 Dihedral : 4.678 43.337 411 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.81 % Allowed : 29.52 % Favored : 66.67 % 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: 2.74 (0.46), residues: 374 helix: 2.70 (0.33), residues: 240 sheet: 0.61 (0.81), residues: 42 loop : -0.01 (0.76), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 316 HIS 0.004 0.001 HIS A 592 PHE 0.025 0.001 PHE A 330 TYR 0.027 0.002 TYR A 675 ARG 0.010 0.001 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.12 seconds wall clock time: 39 minutes 57.41 seconds (2397.41 seconds total)