null Mon 24 Dec 00:12:33 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpz-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:12:38 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 84 and 0 Target number of residues in the AU: 84 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-4.0-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 24.580 4.002 Wilson plot Bfac: 90.47 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1242 reflections ( 97.11 % complete ) and 0 restraints for refining 1287 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3733 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3023 (Rfree = 0.000) for 1287 atoms. Found 1 (6 requested) and removed 138 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 4.00 Search for helices and strands: 0 residues in 0 chains, 1166 seeds are put forward NCS extension: 0 residues added, 1166 seeds are put forward Round 1: 16 peptides, 4 chains. Longest chain 4 peptides. Score 0.167 Round 2: 20 peptides, 5 chains. Longest chain 4 peptides. Score 0.167 Round 3: 16 peptides, 4 chains. Longest chain 4 peptides. Score 0.167 Round 4: 21 peptides, 4 chains. Longest chain 7 peptides. Score 0.259 Round 5: 23 peptides, 4 chains. Longest chain 7 peptides. Score 0.291 Taking the results from Round 5 Chains 4, Residues 19, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2862 restraints for refining 1030 atoms. 2790 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3038 (Rfree = 0.000) for 1030 atoms. Found 1 (4 requested) and removed 71 (2 requested) atoms. Cycle 2: After refmac, R = 0.3032 (Rfree = 0.000) for 959 atoms. Found 1 (4 requested) and removed 12 (2 requested) atoms. Cycle 3: After refmac, R = 0.3023 (Rfree = 0.000) for 946 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 4: After refmac, R = 0.2823 (Rfree = 0.000) for 942 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 5: After refmac, R = 0.2808 (Rfree = 0.000) for 936 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.55 Search for helices and strands: 0 residues in 0 chains, 960 seeds are put forward NCS extension: 0 residues added, 960 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.270 Round 2: 50 peptides, 7 chains. Longest chain 12 peptides. Score 0.462 Round 3: 52 peptides, 8 chains. Longest chain 10 peptides. Score 0.434 Round 4: 58 peptides, 8 chains. Longest chain 9 peptides. Score 0.500 Round 5: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.437 Taking the results from Round 4 Chains 8, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2073 restraints for refining 876 atoms. 1881 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3219 (Rfree = 0.000) for 876 atoms. Found 4 (4 requested) and removed 15 (2 requested) atoms. Cycle 7: After refmac, R = 0.3086 (Rfree = 0.000) for 864 atoms. Found 1 (4 requested) and removed 8 (2 requested) atoms. Cycle 8: After refmac, R = 0.3043 (Rfree = 0.000) for 855 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. Cycle 9: After refmac, R = 0.3063 (Rfree = 0.000) for 847 atoms. Found 0 (4 requested) and removed 11 (2 requested) atoms. Cycle 10: After refmac, R = 0.3047 (Rfree = 0.000) for 835 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.79 Search for helices and strands: 0 residues in 0 chains, 856 seeds are put forward NCS extension: 0 residues added, 856 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.278 Round 2: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.367 Round 3: 62 peptides, 9 chains. Longest chain 12 peptides. Score 0.495 Round 4: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.349 Round 5: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.414 Taking the results from Round 3 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2111 restraints for refining 893 atoms. 1908 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3209 (Rfree = 0.000) for 893 atoms. Found 2 (4 requested) and removed 7 (2 requested) atoms. Cycle 12: After refmac, R = 0.3028 (Rfree = 0.000) for 886 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 13: After refmac, R = 0.2935 (Rfree = 0.000) for 882 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.2886 (Rfree = 0.000) for 877 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2881 (Rfree = 0.000) for 875 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 4.03 Search for helices and strands: 0 residues in 0 chains, 901 seeds are put forward NCS extension: 0 residues added, 901 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.209 Round 2: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.342 Round 3: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.317 Round 4: 54 peptides, 9 chains. Longest chain 8 peptides. Score 0.406 Round 5: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 4 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2219 restraints for refining 914 atoms. 2048 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3558 (Rfree = 0.000) for 914 atoms. Found 2 (4 requested) and removed 17 (2 requested) atoms. Cycle 17: After refmac, R = 0.3374 (Rfree = 0.000) for 899 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.3300 (Rfree = 0.000) for 895 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.3228 (Rfree = 0.000) for 893 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.3205 (Rfree = 0.000) for 889 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.73 Search for helices and strands: 0 residues in 0 chains, 916 seeds are put forward NCS extension: 0 residues added, 916 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.333 Round 2: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.394 Round 3: 52 peptides, 9 chains. Longest chain 14 peptides. Score 0.382 Round 4: 50 peptides, 8 chains. Longest chain 10 peptides. Score 0.411 Round 5: 56 peptides, 9 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 5 Chains 9, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2151 restraints for refining 898 atoms. 1972 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3249 (Rfree = 0.000) for 898 atoms. Found 4 (4 requested) and removed 21 (2 requested) atoms. Cycle 22: After refmac, R = 0.3217 (Rfree = 0.000) for 879 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 23: After refmac, R = 0.3090 (Rfree = 0.000) for 874 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 24: After refmac, R = 0.3055 (Rfree = 0.000) for 869 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 25: After refmac, R = 0.3032 (Rfree = 0.000) for 864 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.87 Search for helices and strands: 0 residues in 0 chains, 887 seeds are put forward NCS extension: 0 residues added, 887 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.291 Round 2: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.345 Round 3: 50 peptides, 8 chains. Longest chain 10 peptides. Score 0.411 Round 4: 55 peptides, 9 chains. Longest chain 10 peptides. Score 0.418 Round 5: 49 peptides, 7 chains. Longest chain 12 peptides. Score 0.451 Taking the results from Round 5 Chains 7, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2218 restraints for refining 920 atoms. 2057 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3237 (Rfree = 0.000) for 920 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 27: After refmac, R = 0.3062 (Rfree = 0.000) for 914 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2974 (Rfree = 0.000) for 910 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2909 (Rfree = 0.000) for 905 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2891 (Rfree = 0.000) for 903 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.02 2.25 Search for helices and strands: 0 residues in 0 chains, 918 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 931 seeds are put forward Round 1: 34 peptides, 6 chains. Longest chain 10 peptides. Score 0.320 Round 2: 35 peptides, 5 chains. Longest chain 11 peptides. Score 0.393 Round 3: 40 peptides, 6 chains. Longest chain 11 peptides. Score 0.398 Round 4: 41 peptides, 6 chains. Longest chain 10 peptides. Score 0.410 Round 5: 45 peptides, 6 chains. Longest chain 12 peptides. Score 0.457 Taking the results from Round 5 Chains 6, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2277 restraints for refining 925 atoms. 2127 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3235 (Rfree = 0.000) for 925 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.3081 (Rfree = 0.000) for 923 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2990 (Rfree = 0.000) for 919 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2917 (Rfree = 0.000) for 916 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2875 (Rfree = 0.000) for 914 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 940 seeds are put forward NCS extension: 0 residues added, 940 seeds are put forward Round 1: 40 peptides, 7 chains. Longest chain 7 peptides. Score 0.341 Round 2: 47 peptides, 8 chains. Longest chain 10 peptides. Score 0.374 Round 3: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.362 Round 4: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.355 Round 5: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.370 Taking the results from Round 2 Chains 8, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2285 restraints for refining 938 atoms. 2137 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3200 (Rfree = 0.000) for 938 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.3098 (Rfree = 0.000) for 934 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.3053 (Rfree = 0.000) for 932 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.3013 (Rfree = 0.000) for 928 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2986 (Rfree = 0.000) for 926 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 937 seeds are put forward NCS extension: 0 residues added, 937 seeds are put forward Round 1: 30 peptides, 6 chains. Longest chain 8 peptides. Score 0.263 Round 2: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.253 Round 3: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 4: 36 peptides, 6 chains. Longest chain 10 peptides. Score 0.347 Round 5: 42 peptides, 9 chains. Longest chain 10 peptides. Score 0.253 Taking the results from Round 4 Chains 6, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2323 restraints for refining 928 atoms. 2209 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3098 (Rfree = 0.000) for 928 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.3050 (Rfree = 0.000) for 925 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2990 (Rfree = 0.000) for 924 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2940 (Rfree = 0.000) for 922 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2928 (Rfree = 0.000) for 921 atoms. Found 0 (4 requested) and removed 21 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.66 Search for helices and strands: 0 residues in 0 chains, 910 seeds are put forward NCS extension: 0 residues added, 910 seeds are put forward Round 1: 22 peptides, 4 chains. Longest chain 10 peptides. Score 0.275 Round 2: 19 peptides, 3 chains. Longest chain 8 peptides. Score 0.301 Round 3: 22 peptides, 3 chains. Longest chain 10 peptides. Score 0.347 Round 4: 21 peptides, 4 chains. Longest chain 7 peptides. Score 0.259 Round 5: 20 peptides, 3 chains. Longest chain 10 peptides. Score 0.317 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 19, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vpz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1242 reflections ( 97.11 % complete ) and 2270 restraints for refining 899 atoms. 2197 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3032 (Rfree = 0.000) for 899 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2948 (Rfree = 0.000) for 897 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2910 (Rfree = 0.000) for 895 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2918 (Rfree = 0.000) for 892 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:32:17 GMT 2018 Job finished. TimeTaking 19.73 Used memory is bytes: 22123856