null Mon 24 Dec 00:50:33 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 2fur-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-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/2fur-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-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 00:50:37 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/2fur-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-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 265 and 0 Target number of residues in the AU: 265 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-3.4-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.65 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: 55.473 3.400 Wilson plot Bfac: 76.06 5955 reflections ( 99.65 % complete ) and 0 restraints for refining 3694 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3124 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2925 (Rfree = 0.000) for 3694 atoms. Found 17 (27 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.70 Search for helices and strands: 0 residues in 0 chains, 3738 seeds are put forward NCS extension: 0 residues added, 3738 seeds are put forward Round 1: 170 peptides, 32 chains. Longest chain 11 peptides. Score 0.354 Round 2: 234 peptides, 35 chains. Longest chain 15 peptides. Score 0.540 Round 3: 253 peptides, 33 chains. Longest chain 19 peptides. Score 0.623 Round 4: 255 peptides, 31 chains. Longest chain 29 peptides. Score 0.652 Round 5: 249 peptides, 33 chains. Longest chain 19 peptides. Score 0.612 Taking the results from Round 4 Chains 31, Residues 224, Estimated correctness of the model 44.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6862 restraints for refining 3040 atoms. 5997 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2524 (Rfree = 0.000) for 3040 atoms. Found 13 (22 requested) and removed 17 (11 requested) atoms. Cycle 2: After refmac, R = 0.2318 (Rfree = 0.000) for 2991 atoms. Found 10 (22 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2212 (Rfree = 0.000) for 2959 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. Cycle 4: After refmac, R = 0.1899 (Rfree = 0.000) for 2945 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. Cycle 5: After refmac, R = 0.1936 (Rfree = 0.000) for 2931 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 3024 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3052 seeds are put forward Round 1: 202 peptides, 34 chains. Longest chain 12 peptides. Score 0.445 Round 2: 253 peptides, 33 chains. Longest chain 20 peptides. Score 0.623 Round 3: 256 peptides, 31 chains. Longest chain 24 peptides. Score 0.655 Round 4: 262 peptides, 33 chains. Longest chain 21 peptides. Score 0.647 Round 5: 250 peptides, 30 chains. Longest chain 18 peptides. Score 0.651 Taking the results from Round 3 Chains 32, Residues 225, Estimated correctness of the model 45.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6716 restraints for refining 2999 atoms. 5817 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2146 (Rfree = 0.000) for 2999 atoms. Found 9 (22 requested) and removed 20 (11 requested) atoms. Cycle 7: After refmac, R = 0.2030 (Rfree = 0.000) for 2975 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.1971 (Rfree = 0.000) for 2962 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. Cycle 9: After refmac, R = 0.1953 (Rfree = 0.000) for 2949 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.1875 (Rfree = 0.000) for 2935 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 3008 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3030 seeds are put forward Round 1: 238 peptides, 34 chains. Longest chain 14 peptides. Score 0.567 Round 2: 246 peptides, 28 chains. Longest chain 20 peptides. Score 0.664 Round 3: 245 peptides, 26 chains. Longest chain 20 peptides. Score 0.684 Round 4: 260 peptides, 30 chains. Longest chain 19 peptides. Score 0.676 Round 5: 263 peptides, 26 chains. Longest chain 21 peptides. Score 0.725 Taking the results from Round 5 Chains 27, Residues 237, Estimated correctness of the model 64.1 % 2 chains (25 residues) have been docked in sequence Building loops using Loopy2018 27 chains (237 residues) following loop building 2 chains (25 residues) in sequence following loop building ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6442 restraints for refining 3041 atoms. 5431 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2202 (Rfree = 0.000) for 3041 atoms. Found 9 (22 requested) and removed 17 (11 requested) atoms. Cycle 12: After refmac, R = 0.2031 (Rfree = 0.000) for 3016 atoms. Found 0 (22 requested) and removed 19 (11 requested) atoms. Cycle 13: After refmac, R = 0.2130 (Rfree = 0.000) for 2990 atoms. Found 6 (21 requested) and removed 13 (11 requested) atoms. Cycle 14: After refmac, R = 0.1836 (Rfree = 0.000) for 2977 atoms. Found 4 (21 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.1792 (Rfree = 0.000) for 2967 atoms. Found 1 (20 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.70 Search for helices and strands: 0 residues in 0 chains, 3038 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3055 seeds are put forward Round 1: 227 peptides, 33 chains. Longest chain 17 peptides. Score 0.546 Round 2: 231 peptides, 30 chains. Longest chain 20 peptides. Score 0.599 Round 3: 248 peptides, 31 chains. Longest chain 19 peptides. Score 0.634 Round 4: 262 peptides, 30 chains. Longest chain 23 peptides. Score 0.681 Round 5: 250 peptides, 27 chains. Longest chain 24 peptides. Score 0.685 Taking the results from Round 5 Chains 29, Residues 223, Estimated correctness of the model 53.9 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6642 restraints for refining 3041 atoms. 5718 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2325 (Rfree = 0.000) for 3041 atoms. Found 14 (20 requested) and removed 17 (11 requested) atoms. Cycle 17: After refmac, R = 0.2136 (Rfree = 0.000) for 3022 atoms. Found 5 (20 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.2051 (Rfree = 0.000) for 3008 atoms. Found 1 (20 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.2020 (Rfree = 0.000) for 2992 atoms. Found 6 (20 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.1950 (Rfree = 0.000) for 2982 atoms. Found 5 (20 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 3047 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3072 seeds are put forward Round 1: 227 peptides, 38 chains. Longest chain 18 peptides. Score 0.473 Round 2: 240 peptides, 29 chains. Longest chain 18 peptides. Score 0.637 Round 3: 250 peptides, 33 chains. Longest chain 19 peptides. Score 0.615 Round 4: 243 peptides, 27 chains. Longest chain 22 peptides. Score 0.668 Round 5: 241 peptides, 29 chains. Longest chain 20 peptides. Score 0.639 Taking the results from Round 4 Chains 27, Residues 216, Estimated correctness of the model 49.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6916 restraints for refining 3041 atoms. 6079 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2159 (Rfree = 0.000) for 3041 atoms. Found 10 (20 requested) and removed 15 (11 requested) atoms. Cycle 22: After refmac, R = 0.2023 (Rfree = 0.000) for 3030 atoms. Found 9 (20 requested) and removed 17 (11 requested) atoms. Cycle 23: After refmac, R = 0.1973 (Rfree = 0.000) for 3014 atoms. Found 11 (20 requested) and removed 16 (11 requested) atoms. Cycle 24: After refmac, R = 0.1819 (Rfree = 0.000) for 3006 atoms. Found 10 (20 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.1796 (Rfree = 0.000) for 3003 atoms. Found 6 (20 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3115 seeds are put forward Round 1: 204 peptides, 29 chains. Longest chain 12 peptides. Score 0.528 Round 2: 213 peptides, 29 chains. Longest chain 19 peptides. Score 0.558 Round 3: 216 peptides, 26 chains. Longest chain 27 peptides. Score 0.608 Round 4: 212 peptides, 28 chains. Longest chain 20 peptides. Score 0.568 Round 5: 228 peptides, 25 chains. Longest chain 21 peptides. Score 0.653 Taking the results from Round 5 Chains 27, Residues 203, Estimated correctness of the model 45.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6739 restraints for refining 3041 atoms. 5915 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2059 (Rfree = 0.000) for 3041 atoms. Found 12 (20 requested) and removed 26 (11 requested) atoms. Cycle 27: After refmac, R = 0.1864 (Rfree = 0.000) for 3017 atoms. Found 17 (20 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.1778 (Rfree = 0.000) for 3015 atoms. Found 5 (20 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.1685 (Rfree = 0.000) for 3005 atoms. Found 3 (20 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1611 (Rfree = 0.000) for 2994 atoms. Found 5 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3062 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3087 seeds are put forward Round 1: 189 peptides, 33 chains. Longest chain 10 peptides. Score 0.412 Round 2: 218 peptides, 32 chains. Longest chain 21 peptides. Score 0.531 Round 3: 215 peptides, 31 chains. Longest chain 14 peptides. Score 0.535 Round 4: 232 peptides, 30 chains. Longest chain 18 peptides. Score 0.602 Round 5: 222 peptides, 31 chains. Longest chain 22 peptides. Score 0.558 Taking the results from Round 4 Chains 30, Residues 202, Estimated correctness of the model 29.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6919 restraints for refining 3041 atoms. 6141 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1958 (Rfree = 0.000) for 3041 atoms. Found 10 (20 requested) and removed 19 (11 requested) atoms. Cycle 32: After refmac, R = 0.1789 (Rfree = 0.000) for 3028 atoms. Found 11 (20 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.1740 (Rfree = 0.000) for 3022 atoms. Found 5 (20 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1670 (Rfree = 0.000) for 3011 atoms. Found 4 (20 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1491 (Rfree = 0.000) for 3003 atoms. Found 5 (20 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3113 seeds are put forward Round 1: 195 peptides, 34 chains. Longest chain 14 peptides. Score 0.419 Round 2: 211 peptides, 34 chains. Longest chain 20 peptides. Score 0.477 Round 3: 214 peptides, 28 chains. Longest chain 25 peptides. Score 0.575 Round 4: 205 peptides, 29 chains. Longest chain 21 peptides. Score 0.532 Round 5: 222 peptides, 30 chains. Longest chain 21 peptides. Score 0.572 Taking the results from Round 3 Chains 28, Residues 186, Estimated correctness of the model 20.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6861 restraints for refining 3041 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1788 (Rfree = 0.000) for 3041 atoms. Found 11 (20 requested) and removed 11 (11 requested) atoms. Cycle 37: After refmac, R = 0.1733 (Rfree = 0.000) for 3034 atoms. Found 9 (20 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.1626 (Rfree = 0.000) for 3029 atoms. Found 7 (20 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1645 (Rfree = 0.000) for 3025 atoms. Found 3 (20 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1545 (Rfree = 0.000) for 3013 atoms. Found 2 (20 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3062 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 3098 seeds are put forward Round 1: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.409 Round 2: 195 peptides, 27 chains. Longest chain 17 peptides. Score 0.528 Round 3: 195 peptides, 29 chains. Longest chain 17 peptides. Score 0.498 Round 4: 193 peptides, 29 chains. Longest chain 17 peptides. Score 0.491 Round 5: 204 peptides, 31 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 2 Chains 27, Residues 168, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6908 restraints for refining 3041 atoms. 6263 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1659 (Rfree = 0.000) for 3041 atoms. Found 8 (20 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.1663 (Rfree = 0.000) for 3029 atoms. Found 10 (20 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1608 (Rfree = 0.000) for 3025 atoms. Found 7 (20 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1573 (Rfree = 0.000) for 3019 atoms. Found 5 (20 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1644 (Rfree = 0.000) for 3010 atoms. Found 7 (20 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3091 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3111 seeds are put forward Round 1: 149 peptides, 28 chains. Longest chain 15 peptides. Score 0.337 Round 2: 176 peptides, 28 chains. Longest chain 10 peptides. Score 0.445 Round 3: 184 peptides, 28 chains. Longest chain 12 peptides. Score 0.474 Round 4: 164 peptides, 27 chains. Longest chain 10 peptides. Score 0.415 Round 5: 178 peptides, 29 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 156, 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 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5955 reflections ( 99.65 % complete ) and 6967 restraints for refining 3041 atoms. 6371 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1561 (Rfree = 0.000) for 3041 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1491 (Rfree = 0.000) for 3027 atoms. Found 0 (20 requested) and removed 9 (11 requested) atoms. Cycle 48: After refmac, R = 0.1451 (Rfree = 0.000) for 3016 atoms. Found 0 (20 requested) and removed 3 (11 requested) atoms. Cycle 49: After refmac, R = 0.1349 (Rfree = 0.000) for 3012 atoms. Found 0 (20 requested) and removed 2 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:25:05 GMT 2018 Job finished. TimeTaking 34.54 Used memory is bytes: 5682584