Starting phenix.real_space_refine on Tue Feb 13 10:14:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c44_16416/02_2024/8c44_16416_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c44_16416/02_2024/8c44_16416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c44_16416/02_2024/8c44_16416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c44_16416/02_2024/8c44_16416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c44_16416/02_2024/8c44_16416_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c44_16416/02_2024/8c44_16416_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 3363 2.51 5 N 896 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5239 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3821 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 12, 'TRANS': 445} Chain breaks: 17 Chain: "C" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.67 Number of scatterers: 5239 At special positions: 0 Unit cell: (64.064, 74.048, 130.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 952 8.00 N 896 7.00 C 3363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 553 " distance=2.07 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1174 " distance=2.04 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 169 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 202 " - " ASN C 47 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 906.8 milliseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 4 sheets defined 56.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 571 through 592 Processing helix chain 'A' and resid 607 through 632 removed outlier: 3.923A pdb=" N LEU A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 removed outlier: 5.447A pdb=" N PHE A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 682 Processing helix chain 'A' and resid 695 through 714 removed outlier: 3.572A pdb=" N ASN A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 762 Processing helix chain 'A' and resid 764 through 768 Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 843 through 846 No H-bonds generated for 'chain 'A' and resid 843 through 846' Processing helix chain 'A' and resid 869 through 891 Processing helix chain 'A' and resid 904 through 923 Processing helix chain 'A' and resid 932 through 949 Processing helix chain 'A' and resid 972 through 981 Processing helix chain 'A' and resid 984 through 991 removed outlier: 3.611A pdb=" N MET A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 991 " --> pdb=" O TRP A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1009 through 1011 No H-bonds generated for 'chain 'A' and resid 1009 through 1011' Processing helix chain 'A' and resid 1014 through 1036 removed outlier: 3.923A pdb=" N LYS A1036 " --> pdb=" O LYS A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1095 removed outlier: 3.743A pdb=" N GLN A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1126 Processing helix chain 'A' and resid 1162 through 1169 Processing helix chain 'C' and resid 59 through 86 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 155 through 158 No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 160 through 166 Processing helix chain 'C' and resid 168 through 175 Processing sheet with id= A, first strand: chain 'A' and resid 504 through 506 Processing sheet with id= B, first strand: chain 'A' and resid 552 through 554 Processing sheet with id= C, first strand: chain 'A' and resid 826 through 828 removed outlier: 3.686A pdb=" N THR A 826 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 132 through 135 removed outlier: 6.610A pdb=" N VAL C 116 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 125 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 114 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 127 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL C 112 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU C 33 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 852 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: 1.51 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1093 1.32 - 1.46: 1702 1.46 - 1.59: 2499 1.59 - 1.72: 24 1.72 - 1.85: 34 Bond restraints: 5352 Sorted by residual: bond pdb=" C THR A1154 " pdb=" N PRO A1155 " ideal model delta sigma weight residual 1.331 1.396 -0.065 1.31e-02 5.83e+03 2.50e+01 bond pdb=" N VAL C 124 " pdb=" CA VAL C 124 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.07e-02 8.73e+03 2.17e+01 bond pdb=" C ILE A 639 " pdb=" N PRO A 640 " ideal model delta sigma weight residual 1.330 1.386 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" N PRO A 640 " pdb=" CD PRO A 640 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CB ILE A1012 " pdb=" CG1 ILE A1012 " ideal model delta sigma weight residual 1.530 1.451 0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 5347 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.95: 187 106.95 - 113.82: 2792 113.82 - 120.69: 2575 120.69 - 127.56: 1563 127.56 - 134.43: 72 Bond angle restraints: 7189 Sorted by residual: angle pdb=" N PRO C 22 " pdb=" CA PRO C 22 " pdb=" C PRO C 22 " ideal model delta sigma weight residual 113.53 102.47 11.06 1.39e+00 5.18e-01 6.33e+01 angle pdb=" C THR A1006 " pdb=" N PRO A1007 " pdb=" CA PRO A1007 " ideal model delta sigma weight residual 120.21 127.27 -7.06 9.60e-01 1.09e+00 5.41e+01 angle pdb=" C ARG C 127 " pdb=" N PRO C 128 " pdb=" CA PRO C 128 " ideal model delta sigma weight residual 119.84 128.85 -9.01 1.25e+00 6.40e-01 5.20e+01 angle pdb=" C GLY C 43 " pdb=" N PRO C 44 " pdb=" CA PRO C 44 " ideal model delta sigma weight residual 120.21 126.84 -6.63 9.60e-01 1.09e+00 4.77e+01 angle pdb=" C THR A 823 " pdb=" N PRO A 824 " pdb=" CA PRO A 824 " ideal model delta sigma weight residual 119.78 126.72 -6.94 1.03e+00 9.43e-01 4.54e+01 ... (remaining 7184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 3152 32.24 - 64.48: 62 64.48 - 96.71: 7 96.71 - 128.95: 0 128.95 - 161.19: 1 Dihedral angle restraints: 3222 sinusoidal: 1394 harmonic: 1828 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 710 " pdb=" CB CYS A 710 " ideal model delta sinusoidal sigma weight residual -86.00 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" C3 PTY C 201 " pdb=" O11 PTY C 201 " pdb=" P1 PTY C 201 " pdb=" O12 PTY C 201 " ideal model delta sinusoidal sigma weight residual 300.23 139.04 161.19 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CD ARG C 20 " pdb=" NE ARG C 20 " pdb=" CZ ARG C 20 " pdb=" NH1 ARG C 20 " ideal model delta sinusoidal sigma weight residual 0.00 -36.88 36.88 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 3219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 519 0.095 - 0.191: 202 0.191 - 0.286: 32 0.286 - 0.381: 1 0.381 - 0.477: 3 Chirality restraints: 757 Sorted by residual: chirality pdb=" CB ILE A 639 " pdb=" CA ILE A 639 " pdb=" CG1 ILE A 639 " pdb=" CG2 ILE A 639 " both_signs ideal model delta sigma weight residual False 2.64 3.12 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2 NAG C 202 " pdb=" C1 NAG C 202 " pdb=" C3 NAG C 202 " pdb=" N2 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.49 -2.91 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C1 NAG C 202 " pdb=" ND2 ASN C 47 " pdb=" C2 NAG C 202 " pdb=" O5 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 754 not shown) Planarity restraints: 895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 20 " 0.647 9.50e-02 1.11e+02 2.90e-01 5.13e+01 pdb=" NE ARG C 20 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 20 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " -0.556 9.50e-02 1.11e+02 2.49e-01 3.79e+01 pdb=" NE ARG A1017 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 176 " 0.026 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" C HIS C 176 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS C 176 " 0.032 2.00e-02 2.50e+03 pdb=" OXT HIS C 176 " 0.032 2.00e-02 2.50e+03 ... (remaining 892 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1753 2.85 - 3.36: 5196 3.36 - 3.87: 9331 3.87 - 4.39: 10903 4.39 - 4.90: 17214 Nonbonded interactions: 44397 Sorted by model distance: nonbonded pdb=" NZ LYS A1015 " pdb=" OD1 ASP A1112 " model vdw 2.336 2.520 nonbonded pdb=" NZ LYS A 745 " pdb=" OD1 ASP A1009 " model vdw 2.388 2.520 nonbonded pdb=" N ASP A 984 " pdb=" OD1 ASP A 984 " model vdw 2.407 2.520 nonbonded pdb=" NZ LYS A 827 " pdb=" OE2 GLU A 838 " model vdw 2.421 2.520 nonbonded pdb=" OD2 ASP A 572 " pdb=" NZ LYS A 642 " model vdw 2.444 2.520 ... (remaining 44392 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: 4.290 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: 15.270 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.620 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 0.020 0.123 5352 Z= 1.271 Angle : 1.659 19.848 7189 Z= 1.122 Chirality : 0.098 0.477 757 Planarity : 0.015 0.290 894 Dihedral : 12.787 161.189 2015 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.54 % Allowed : 2.86 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.28 (0.34), residues: 584 helix: 1.44 (0.26), residues: 331 sheet: 0.62 (0.66), residues: 57 loop : 0.03 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.008 TRP C 133 HIS 0.007 0.002 HIS A1167 PHE 0.025 0.005 PHE A 615 TYR 0.047 0.007 TYR C 154 ARG 0.007 0.001 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 182 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7285 (mttt) cc_final: 0.6984 (mmtm) REVERT: A 1172 MET cc_start: 0.7568 (mmp) cc_final: 0.6645 (mmt) REVERT: C 75 GLN cc_start: 0.7771 (mt0) cc_final: 0.7216 (tt0) REVERT: C 160 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6412 (mt-10) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.2646 time to fit residues: 58.6152 Evaluate side-chains 96 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1174 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 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 536 ASN A 609 ASN A 621 GLN A 713 ASN A 716 ASN A 746 GLN A 749 GLN C 85 GLN C 174 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5352 Z= 0.271 Angle : 0.626 7.405 7189 Z= 0.341 Chirality : 0.043 0.192 757 Planarity : 0.004 0.034 894 Dihedral : 9.284 151.089 728 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.50 % Allowed : 9.29 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.17 (0.33), residues: 584 helix: 2.40 (0.26), residues: 333 sheet: -0.24 (0.53), residues: 72 loop : 0.43 (0.48), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 669 HIS 0.010 0.002 HIS C 84 PHE 0.016 0.002 PHE A 651 TYR 0.025 0.002 TYR A1120 ARG 0.005 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7443 (mttt) cc_final: 0.7047 (mmtm) REVERT: A 840 PHE cc_start: 0.7659 (m-80) cc_final: 0.7133 (m-80) REVERT: A 848 MET cc_start: 0.7829 (mmm) cc_final: 0.7242 (mmt) REVERT: A 1090 LYS cc_start: 0.6736 (tppt) cc_final: 0.6054 (pttp) outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 0.2214 time to fit residues: 36.0043 Evaluate side-chains 90 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5352 Z= 0.243 Angle : 0.576 9.676 7189 Z= 0.310 Chirality : 0.041 0.161 757 Planarity : 0.004 0.037 894 Dihedral : 8.096 122.597 728 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.50 % Allowed : 13.75 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.98 (0.34), residues: 584 helix: 2.24 (0.26), residues: 345 sheet: -0.58 (0.53), residues: 73 loop : 0.33 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 978 HIS 0.004 0.001 HIS C 84 PHE 0.021 0.002 PHE A 655 TYR 0.016 0.002 TYR A1120 ARG 0.005 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7404 (mttt) cc_final: 0.7105 (mmtm) REVERT: A 840 PHE cc_start: 0.7598 (m-80) cc_final: 0.7132 (m-80) REVERT: A 1090 LYS cc_start: 0.6453 (tppt) cc_final: 0.5903 (pttp) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.1793 time to fit residues: 24.3037 Evaluate side-chains 89 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.0020 chunk 29 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 886 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5352 Z= 0.203 Angle : 0.525 8.468 7189 Z= 0.282 Chirality : 0.039 0.168 757 Planarity : 0.003 0.036 894 Dihedral : 7.520 97.517 728 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.75 % Allowed : 12.68 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.03 (0.35), residues: 584 helix: 2.29 (0.27), residues: 344 sheet: -0.64 (0.54), residues: 73 loop : 0.42 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.029 0.002 PHE A 655 TYR 0.015 0.002 TYR A1120 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7404 (mttt) cc_final: 0.7104 (mmtm) REVERT: A 840 PHE cc_start: 0.7546 (m-80) cc_final: 0.7165 (m-80) REVERT: A 848 MET cc_start: 0.7982 (mmm) cc_final: 0.7323 (mmm) REVERT: A 915 TYR cc_start: 0.8008 (t80) cc_final: 0.7642 (t80) REVERT: A 1090 LYS cc_start: 0.6120 (tppt) cc_final: 0.5684 (pttt) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.1660 time to fit residues: 22.2821 Evaluate side-chains 96 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5352 Z= 0.277 Angle : 0.578 9.950 7189 Z= 0.306 Chirality : 0.040 0.172 757 Planarity : 0.003 0.033 894 Dihedral : 7.381 81.860 728 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.21 % Allowed : 14.64 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.60 (0.34), residues: 584 helix: 1.98 (0.26), residues: 344 sheet: -0.87 (0.55), residues: 73 loop : 0.16 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 978 HIS 0.003 0.001 HIS A 702 PHE 0.021 0.002 PHE A 655 TYR 0.016 0.002 TYR A1120 ARG 0.005 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7412 (mttt) cc_final: 0.7102 (mmtm) REVERT: A 840 PHE cc_start: 0.7600 (m-80) cc_final: 0.7247 (m-80) REVERT: A 848 MET cc_start: 0.7998 (mmm) cc_final: 0.7360 (mmm) REVERT: A 1090 LYS cc_start: 0.6096 (tppt) cc_final: 0.5643 (pttt) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.1869 time to fit residues: 24.0958 Evaluate side-chains 87 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 14 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5352 Z= 0.234 Angle : 0.553 8.743 7189 Z= 0.290 Chirality : 0.039 0.158 757 Planarity : 0.003 0.031 894 Dihedral : 7.036 69.053 728 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.39 % Allowed : 15.89 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.64 (0.35), residues: 584 helix: 2.10 (0.27), residues: 341 sheet: -1.11 (0.54), residues: 73 loop : 0.14 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.022 0.002 PHE A 655 TYR 0.014 0.002 TYR A1120 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 PHE cc_start: 0.7574 (m-80) cc_final: 0.7230 (m-80) REVERT: A 848 MET cc_start: 0.7922 (mmm) cc_final: 0.7371 (mmm) REVERT: A 1090 LYS cc_start: 0.6175 (tppt) cc_final: 0.5686 (pttt) outliers start: 19 outliers final: 15 residues processed: 91 average time/residue: 0.1832 time to fit residues: 21.8467 Evaluate side-chains 87 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.0070 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5352 Z= 0.148 Angle : 0.495 9.738 7189 Z= 0.260 Chirality : 0.037 0.160 757 Planarity : 0.003 0.030 894 Dihedral : 6.611 58.710 728 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.86 % Allowed : 16.43 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.97 (0.35), residues: 584 helix: 2.39 (0.27), residues: 346 sheet: -1.28 (0.53), residues: 75 loop : 0.35 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 978 HIS 0.003 0.000 HIS A1167 PHE 0.020 0.001 PHE A 655 TYR 0.013 0.001 TYR C 72 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6881 (mttp) cc_final: 0.6544 (mptt) REVERT: A 840 PHE cc_start: 0.7541 (m-80) cc_final: 0.7138 (m-80) REVERT: A 848 MET cc_start: 0.7948 (mmm) cc_final: 0.7390 (mmm) REVERT: A 1090 LYS cc_start: 0.6309 (tppt) cc_final: 0.5845 (pttt) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.1609 time to fit residues: 21.4585 Evaluate side-chains 92 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5352 Z= 0.273 Angle : 0.564 9.679 7189 Z= 0.297 Chirality : 0.040 0.155 757 Planarity : 0.003 0.026 894 Dihedral : 6.872 56.232 728 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.04 % Allowed : 16.96 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.51 (0.35), residues: 584 helix: 1.98 (0.27), residues: 346 sheet: -1.48 (0.53), residues: 75 loop : 0.26 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 978 HIS 0.003 0.001 HIS A 702 PHE 0.018 0.002 PHE A 655 TYR 0.016 0.002 TYR A1120 ARG 0.003 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 840 PHE cc_start: 0.7663 (m-80) cc_final: 0.7346 (m-80) REVERT: A 848 MET cc_start: 0.7896 (mmm) cc_final: 0.7314 (mmm) REVERT: A 911 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7010 (tt) REVERT: A 1090 LYS cc_start: 0.6179 (tppt) cc_final: 0.5757 (pttt) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.1693 time to fit residues: 20.4944 Evaluate side-chains 86 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5352 Z= 0.252 Angle : 0.573 10.158 7189 Z= 0.301 Chirality : 0.040 0.152 757 Planarity : 0.003 0.025 894 Dihedral : 6.902 52.768 728 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.86 % Allowed : 17.86 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.38 (0.35), residues: 584 helix: 1.88 (0.27), residues: 346 sheet: -1.53 (0.53), residues: 74 loop : 0.20 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.028 0.002 PHE C 123 TYR 0.015 0.002 TYR A1120 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 PHE cc_start: 0.7657 (m-80) cc_final: 0.7333 (m-80) REVERT: A 848 MET cc_start: 0.7874 (mmm) cc_final: 0.7321 (mmm) REVERT: A 911 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.6956 (tt) REVERT: A 1090 LYS cc_start: 0.6345 (tppt) cc_final: 0.5908 (pttt) outliers start: 16 outliers final: 14 residues processed: 87 average time/residue: 0.1702 time to fit residues: 19.6631 Evaluate side-chains 85 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5352 Z= 0.254 Angle : 0.584 10.217 7189 Z= 0.304 Chirality : 0.040 0.165 757 Planarity : 0.003 0.031 894 Dihedral : 6.865 53.716 728 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.21 % Allowed : 18.39 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.26 (0.35), residues: 584 helix: 1.79 (0.27), residues: 346 sheet: -1.53 (0.53), residues: 74 loop : 0.11 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.022 0.002 PHE C 123 TYR 0.015 0.002 TYR A1120 ARG 0.009 0.001 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 PHE cc_start: 0.7622 (m-80) cc_final: 0.7304 (m-80) REVERT: A 848 MET cc_start: 0.7890 (mmm) cc_final: 0.7336 (mmm) REVERT: A 911 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.6997 (tt) REVERT: A 1090 LYS cc_start: 0.6308 (tppt) cc_final: 0.5872 (pttt) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.1723 time to fit residues: 19.9723 Evaluate side-chains 85 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.198881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.166081 restraints weight = 5974.816| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.72 r_work: 0.3993 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5352 Z= 0.254 Angle : 0.583 10.031 7189 Z= 0.303 Chirality : 0.040 0.165 757 Planarity : 0.003 0.041 894 Dihedral : 6.934 59.278 728 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.86 % Allowed : 18.21 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.23 (0.35), residues: 584 helix: 1.76 (0.27), residues: 346 sheet: -1.55 (0.54), residues: 75 loop : 0.11 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.022 0.002 PHE C 123 TYR 0.015 0.002 TYR A1120 ARG 0.009 0.001 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.63 seconds wall clock time: 31 minutes 48.25 seconds (1908.25 seconds total)