Starting phenix.real_space_refine (version: dev) on Fri Feb 17 20:35:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/02_2023/7lrc_23494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/02_2023/7lrc_23494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/02_2023/7lrc_23494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/02_2023/7lrc_23494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/02_2023/7lrc_23494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/02_2023/7lrc_23494_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "B PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6202 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.12, per 1000 atoms: 0.66 Number of scatterers: 6202 At special positions: 0 Unit cell: (115.867, 94.607, 74.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 36 16.00 Mg 2 11.99 O 1126 8.00 N 1040 7.00 C 3996 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 - 3.50 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 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 903.1 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 2 sheets defined 63.3% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 685 through 690 removed outlier: 4.162A pdb=" N ASN B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 710 through 722 Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 732 through 745 Processing helix chain 'B' and resid 754 through 769 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 823 through 834 Processing helix chain 'B' and resid 845 through 850 Processing helix chain 'B' and resid 854 through 858 Processing helix chain 'B' and resid 864 through 879 Processing helix chain 'B' and resid 881 through 883 No H-bonds generated for 'chain 'B' and resid 881 through 883' Processing helix chain 'B' and resid 891 through 908 removed outlier: 3.679A pdb=" N THR B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 925 Processing helix chain 'B' and resid 935 through 955 removed outlier: 3.585A pdb=" N ILE B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Proline residue: B 954 - end of helix Processing helix chain 'B' and resid 958 through 982 Processing helix chain 'B' and resid 997 through 1007 Processing helix chain 'B' and resid 1009 through 1019 Processing helix chain 'B' and resid 1074 through 1099 Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 685 through 690 removed outlier: 4.163A pdb=" N ASN C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 724 through 727 No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'C' and resid 754 through 769 Processing helix chain 'C' and resid 817 through 819 No H-bonds generated for 'chain 'C' and resid 817 through 819' Processing helix chain 'C' and resid 823 through 834 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 864 through 879 Processing helix chain 'C' and resid 881 through 883 No H-bonds generated for 'chain 'C' and resid 881 through 883' Processing helix chain 'C' and resid 891 through 908 removed outlier: 3.679A pdb=" N THR C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 925 Processing helix chain 'C' and resid 935 through 955 removed outlier: 3.585A pdb=" N ILE C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY C 953 " --> pdb=" O ALA C 949 " (cutoff:3.500A) Proline residue: C 954 - end of helix Processing helix chain 'C' and resid 958 through 982 Processing helix chain 'C' and resid 997 through 1007 Processing helix chain 'C' and resid 1009 through 1019 Processing helix chain 'C' and resid 1074 through 1099 Processing helix chain 'D' and resid 552 through 558 Processing sheet with id= A, first strand: chain 'B' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS B1070 " --> pdb=" O VAL B1027 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS C1070 " --> pdb=" O VAL C1027 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 930 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: 1.81 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1278 1.33 - 1.45: 1530 1.45 - 1.57: 3492 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6358 Sorted by residual: bond pdb=" N16 X5M C2003 " pdb=" N17 X5M C2003 " ideal model delta sigma weight residual 1.354 1.394 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" N16 X5M B2003 " pdb=" N17 X5M B2003 " ideal model delta sigma weight residual 1.354 1.394 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C15 X5M C2003 " pdb=" C21 X5M C2003 " ideal model delta sigma weight residual 1.505 1.544 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C15 X5M B2003 " pdb=" C21 X5M B2003 " ideal model delta sigma weight residual 1.505 1.544 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C11 X5M C2003 " pdb=" N12 X5M C2003 " ideal model delta sigma weight residual 1.454 1.427 0.027 2.00e-02 2.50e+03 1.81e+00 ... (remaining 6353 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.33: 260 107.33 - 114.00: 3524 114.00 - 120.67: 2797 120.67 - 127.34: 1957 127.34 - 134.00: 92 Bond angle restraints: 8630 Sorted by residual: angle pdb=" C05 X5M B2003 " pdb=" C04 X5M B2003 " pdb=" N03 X5M B2003 " ideal model delta sigma weight residual 115.49 104.75 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C05 X5M C2003 " pdb=" C04 X5M C2003 " pdb=" N03 X5M C2003 " ideal model delta sigma weight residual 115.49 104.75 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C PRO C 988 " pdb=" N PHE C 989 " pdb=" CA PHE C 989 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.31e+00 angle pdb=" C PRO B 988 " pdb=" N PHE B 989 " pdb=" CA PHE B 989 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.31e+00 angle pdb=" C07 X5M C2003 " pdb=" C06 X5M C2003 " pdb=" N03 X5M C2003 " ideal model delta sigma weight residual 122.57 116.98 5.59 3.00e+00 1.11e-01 3.47e+00 ... (remaining 8625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.15: 3487 11.15 - 22.31: 189 22.31 - 33.46: 52 33.46 - 44.61: 10 44.61 - 55.76: 4 Dihedral angle restraints: 3742 sinusoidal: 1512 harmonic: 2230 Sorted by residual: dihedral pdb=" CA MET C 835 " pdb=" C MET C 835 " pdb=" N HIS C 836 " pdb=" CA HIS C 836 " ideal model delta harmonic sigma weight residual -180.00 -166.06 -13.94 0 5.00e+00 4.00e-02 7.77e+00 dihedral pdb=" CA MET B 835 " pdb=" C MET B 835 " pdb=" N HIS B 836 " pdb=" CA HIS B 836 " ideal model delta harmonic sigma weight residual -180.00 -166.06 -13.94 0 5.00e+00 4.00e-02 7.77e+00 dihedral pdb=" N MET B 944 " pdb=" CA MET B 944 " pdb=" CB MET B 944 " pdb=" CG MET B 944 " ideal model delta sinusoidal sigma weight residual -60.00 -93.08 33.08 3 1.50e+01 4.44e-03 5.50e+00 ... (remaining 3739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 744 0.042 - 0.083: 154 0.083 - 0.125: 29 0.125 - 0.167: 3 0.167 - 0.208: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" C21 X5M C2003 " pdb=" C15 X5M C2003 " pdb=" C20 X5M C2003 " pdb=" C22 X5M C2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C21 X5M B2003 " pdb=" C15 X5M B2003 " pdb=" C20 X5M B2003 " pdb=" C22 X5M B2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE B 821 " pdb=" N ILE B 821 " pdb=" C ILE B 821 " pdb=" CB ILE B 821 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 929 not shown) Planarity restraints: 1114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 X5M B2003 " 0.057 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C04 X5M B2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M B2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M B2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 X5M C2003 " 0.057 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C04 X5M C2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M C2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M C2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 X5M C2003 " 0.014 2.00e-02 2.50e+03 5.86e-02 4.29e+01 pdb=" C20 X5M C2003 " 0.016 2.00e-02 2.50e+03 pdb=" N16 X5M C2003 " -0.069 2.00e-02 2.50e+03 pdb=" N17 X5M C2003 " 0.094 2.00e-02 2.50e+03 pdb=" O19 X5M C2003 " -0.055 2.00e-02 2.50e+03 ... (remaining 1111 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 30 2.42 - 3.04: 4066 3.04 - 3.66: 9321 3.66 - 4.28: 14640 4.28 - 4.90: 24181 Nonbonded interactions: 52238 Sorted by model distance: nonbonded pdb=" OD1 ASP B 950 " pdb="MN MN B2001 " model vdw 1.795 2.320 nonbonded pdb=" OD1 ASP C 950 " pdb="MN MN C2001 " model vdw 1.795 2.320 nonbonded pdb=" OD2 ASP B 837 " pdb="MN MN B2001 " model vdw 2.046 2.320 nonbonded pdb=" OD2 ASP C 837 " pdb="MN MN C2001 " model vdw 2.046 2.320 nonbonded pdb=" OD1 ASP C 837 " pdb="MG MG C2002 " model vdw 2.142 2.170 ... (remaining 52233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 Mg 2 5.21 5 S 36 5.16 5 C 3996 2.51 5 N 1040 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.040 Check model and map are aligned: 0.100 Process input model: 20.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.002 0.040 6358 Z= 0.162 Angle : 0.495 10.737 8630 Z= 0.262 Chirality : 0.036 0.208 932 Planarity : 0.006 0.100 1114 Dihedral : 7.938 55.764 2298 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 0.30 % 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: 3.49 (0.31), residues: 746 helix: 2.83 (0.22), residues: 504 sheet: None (None), residues: 0 loop : 1.32 (0.42), residues: 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.796 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 1.2101 time to fit residues: 91.8301 Evaluate side-chains 42 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 999 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 6358 Z= 0.138 Angle : 0.456 7.131 8630 Z= 0.216 Chirality : 0.036 0.136 932 Planarity : 0.003 0.039 1114 Dihedral : 3.755 37.729 822 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 0.90 % 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: 3.53 (0.31), residues: 746 helix: 2.80 (0.23), residues: 506 sheet: None (None), residues: 0 loop : 1.48 (0.41), residues: 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.825 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.9451 time to fit residues: 47.2074 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 23 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 6358 Z= 0.130 Angle : 0.441 7.609 8630 Z= 0.210 Chirality : 0.035 0.134 932 Planarity : 0.003 0.040 1114 Dihedral : 3.579 31.806 822 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 1.81 % 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: 3.70 (0.30), residues: 746 helix: 2.93 (0.23), residues: 496 sheet: None (None), residues: 0 loop : 1.61 (0.41), residues: 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.687 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 0.9943 time to fit residues: 53.9266 Evaluate side-chains 46 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 6358 Z= 0.231 Angle : 0.496 7.081 8630 Z= 0.240 Chirality : 0.037 0.129 932 Planarity : 0.003 0.041 1114 Dihedral : 3.652 26.848 822 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 1.96 % 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: 3.68 (0.31), residues: 746 helix: 2.97 (0.23), residues: 494 sheet: None (None), residues: 0 loop : 1.49 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.811 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.9498 time to fit residues: 53.2598 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.0010 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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: 0.7551 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6358 Z= 0.136 Angle : 0.488 9.485 8630 Z= 0.229 Chirality : 0.036 0.159 932 Planarity : 0.003 0.041 1114 Dihedral : 3.564 27.550 822 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 1.81 % 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: 3.63 (0.30), residues: 746 helix: 2.94 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.45 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 44 average time/residue: 1.0932 time to fit residues: 51.7676 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.2192 time to fit residues: 3.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7595 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6358 Z= 0.195 Angle : 0.515 10.091 8630 Z= 0.240 Chirality : 0.036 0.136 932 Planarity : 0.003 0.042 1114 Dihedral : 3.540 25.718 822 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 1.96 % 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: 3.65 (0.31), residues: 746 helix: 2.98 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.39 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.855 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 44 average time/residue: 1.0561 time to fit residues: 50.3136 Evaluate side-chains 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.9821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 6358 Z= 0.143 Angle : 0.518 11.358 8630 Z= 0.234 Chirality : 0.036 0.134 932 Planarity : 0.003 0.042 1114 Dihedral : 3.445 26.084 822 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 2.11 % 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: 3.66 (0.31), residues: 746 helix: 2.99 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.41 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 33 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 43 average time/residue: 1.0655 time to fit residues: 49.5976 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.0804 time to fit residues: 3.2066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7579 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 6358 Z= 0.162 Angle : 0.545 11.947 8630 Z= 0.242 Chirality : 0.036 0.164 932 Planarity : 0.003 0.042 1114 Dihedral : 3.434 25.294 822 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer Outliers : 1.20 % 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: 3.64 (0.30), residues: 746 helix: 3.00 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.32 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.776 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 1.1140 time to fit residues: 48.0361 Evaluate side-chains 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.0649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 68 optimal weight: 0.0050 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS C 740 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 6358 Z= 0.129 Angle : 0.545 12.804 8630 Z= 0.242 Chirality : 0.036 0.141 932 Planarity : 0.003 0.043 1114 Dihedral : 3.375 25.573 822 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 1.05 % 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: 3.58 (0.30), residues: 746 helix: 2.95 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.32 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.820 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 1.1096 time to fit residues: 47.6024 Evaluate side-chains 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.9606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6358 Z= 0.176 Angle : 0.589 13.344 8630 Z= 0.261 Chirality : 0.037 0.147 932 Planarity : 0.003 0.042 1114 Dihedral : 3.431 24.220 822 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 0.90 % 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: 3.56 (0.31), residues: 746 helix: 2.95 (0.23), residues: 494 sheet: None (None), residues: 0 loop : 1.27 (0.41), residues: 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.804 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 1.1290 time to fit residues: 46.1381 Evaluate side-chains 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3193 r_free = 0.3193 target = 0.044174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.036667 restraints weight = 32031.534| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.02 r_work: 0.2811 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 6358 Z= 0.148 Angle : 0.585 13.030 8630 Z= 0.257 Chirality : 0.036 0.142 932 Planarity : 0.003 0.042 1114 Dihedral : 3.364 24.468 822 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 1.05 % 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: 3.50 (0.30), residues: 746 helix: 2.89 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.28 (0.41), residues: 252 =============================================================================== Job complete usr+sys time: 1864.36 seconds wall clock time: 34 minutes 37.28 seconds (2077.28 seconds total)