null Mon 24 Dec 00:41:28 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 2h1q-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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/2h1q-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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 00:41:33 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/2h1q-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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 372 and 0 Target number of residues in the AU: 372 Target solvent content: 0.6820 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.54 Input MTZ file: 2h1q-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4320 target number of atoms Had to go as low as 0.75 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: 28.996 4.001 Wilson plot Bfac: 102.58 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 5367 reflections ( 99.54 % complete ) and 0 restraints for refining 4789 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3550 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3190 (Rfree = 0.000) for 4789 atoms. Found 22 (22 requested) and removed 43 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.00 3.79 Search for helices and strands: 0 residues in 0 chains, 4843 seeds are put forward NCS extension: 0 residues added, 4843 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 11 peptides. Score 0.234 Round 2: 158 peptides, 30 chains. Longest chain 10 peptides. Score 0.292 Round 3: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.325 Round 4: 178 peptides, 27 chains. Longest chain 14 peptides. Score 0.388 Round 5: 177 peptides, 28 chains. Longest chain 15 peptides. Score 0.373 Taking the results from Round 4 Chains 27, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 10044 restraints for refining 3846 atoms. 9467 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3036 (Rfree = 0.000) for 3846 atoms. Found 17 (18 requested) and removed 34 (9 requested) atoms. Cycle 2: After refmac, R = 0.3105 (Rfree = 0.000) for 3754 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 3: After refmac, R = 0.3009 (Rfree = 0.000) for 3689 atoms. Found 11 (17 requested) and removed 27 (8 requested) atoms. Cycle 4: After refmac, R = 0.2732 (Rfree = 0.000) for 3630 atoms. Found 10 (17 requested) and removed 28 (8 requested) atoms. Cycle 5: After refmac, R = 0.2564 (Rfree = 0.000) for 3588 atoms. Found 11 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.97 3.76 Search for helices and strands: 0 residues in 0 chains, 3666 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3682 seeds are put forward Round 1: 151 peptides, 33 chains. Longest chain 9 peptides. Score 0.231 Round 2: 187 peptides, 34 chains. Longest chain 11 peptides. Score 0.326 Round 3: 212 peptides, 37 chains. Longest chain 15 peptides. Score 0.360 Round 4: 192 peptides, 33 chains. Longest chain 12 peptides. Score 0.353 Round 5: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.353 Taking the results from Round 3 Chains 37, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7468 restraints for refining 3205 atoms. 6805 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2903 (Rfree = 0.000) for 3205 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 7: After refmac, R = 0.2785 (Rfree = 0.000) for 3129 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. Cycle 8: After refmac, R = 0.2685 (Rfree = 0.000) for 3084 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 9: After refmac, R = 0.2641 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 37 (7 requested) atoms. Cycle 10: After refmac, R = 0.2658 (Rfree = 0.000) for 3023 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.06 3.85 Search for helices and strands: 0 residues in 0 chains, 3110 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3129 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 16 peptides. Score 0.320 Round 2: 215 peptides, 34 chains. Longest chain 11 peptides. Score 0.403 Round 3: 215 peptides, 35 chains. Longest chain 12 peptides. Score 0.391 Round 4: 201 peptides, 34 chains. Longest chain 14 peptides. Score 0.365 Round 5: 209 peptides, 32 chains. Longest chain 15 peptides. Score 0.410 Taking the results from Round 5 Chains 32, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7741 restraints for refining 3334 atoms. 7065 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2623 (Rfree = 0.000) for 3334 atoms. Found 9 (15 requested) and removed 280 (7 requested) atoms. Cycle 12: After refmac, R = 0.2709 (Rfree = 0.000) for 3027 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 13: After refmac, R = 0.2621 (Rfree = 0.000) for 2992 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 14: After refmac, R = 0.2620 (Rfree = 0.000) for 2960 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 15: After refmac, R = 0.2482 (Rfree = 0.000) for 2934 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.93 3.73 Search for helices and strands: 0 residues in 0 chains, 3057 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3068 seeds are put forward Round 1: 209 peptides, 40 chains. Longest chain 13 peptides. Score 0.316 Round 2: 200 peptides, 35 chains. Longest chain 10 peptides. Score 0.351 Round 3: 208 peptides, 36 chains. Longest chain 11 peptides. Score 0.361 Round 4: 199 peptides, 32 chains. Longest chain 12 peptides. Score 0.384 Round 5: 212 peptides, 35 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 4 Chains 32, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7084 restraints for refining 3178 atoms. 6448 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2759 (Rfree = 0.000) for 3178 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. Cycle 17: After refmac, R = 0.2534 (Rfree = 0.000) for 3126 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 18: After refmac, R = 0.2541 (Rfree = 0.000) for 3105 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.2525 (Rfree = 0.000) for 3087 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 20: After refmac, R = 0.2423 (Rfree = 0.000) for 3072 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.93 3.73 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3186 seeds are put forward Round 1: 170 peptides, 37 chains. Longest chain 8 peptides. Score 0.238 Round 2: 195 peptides, 36 chains. Longest chain 10 peptides. Score 0.325 Round 3: 203 peptides, 36 chains. Longest chain 11 peptides. Score 0.347 Round 4: 213 peptides, 36 chains. Longest chain 15 peptides. Score 0.374 Round 5: 220 peptides, 38 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 4 Chains 36, Residues 177, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7184 restraints for refining 3292 atoms. 6420 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2599 (Rfree = 0.000) for 3292 atoms. Found 15 (15 requested) and removed 114 (7 requested) atoms. Cycle 22: After refmac, R = 0.2929 (Rfree = 0.000) for 3155 atoms. Found 15 (15 requested) and removed 35 (7 requested) atoms. Cycle 23: After refmac, R = 0.2625 (Rfree = 0.000) for 3110 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 24: After refmac, R = 0.2430 (Rfree = 0.000) for 3082 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 25: After refmac, R = 0.2375 (Rfree = 0.000) for 3060 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.28 4.06 Search for helices and strands: 0 residues in 0 chains, 3137 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3160 seeds are put forward Round 1: 180 peptides, 36 chains. Longest chain 12 peptides. Score 0.281 Round 2: 204 peptides, 35 chains. Longest chain 16 peptides. Score 0.362 Round 3: 197 peptides, 34 chains. Longest chain 11 peptides. Score 0.354 Round 4: 201 peptides, 34 chains. Longest chain 12 peptides. Score 0.365 Round 5: 201 peptides, 31 chains. Longest chain 15 peptides. Score 0.401 Taking the results from Round 5 Chains 31, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7643 restraints for refining 3364 atoms. 6994 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2640 (Rfree = 0.000) for 3364 atoms. Found 15 (15 requested) and removed 53 (7 requested) atoms. Cycle 27: After refmac, R = 0.2487 (Rfree = 0.000) for 3298 atoms. Found 15 (15 requested) and removed 46 (7 requested) atoms. Cycle 28: After refmac, R = 0.2496 (Rfree = 0.000) for 3254 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 29: After refmac, R = 0.2584 (Rfree = 0.000) for 3233 atoms. Found 15 (15 requested) and removed 28 (7 requested) atoms. Cycle 30: After refmac, R = 0.2412 (Rfree = 0.000) for 3212 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.12 3.91 Search for helices and strands: 0 residues in 0 chains, 3288 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3303 seeds are put forward Round 1: 171 peptides, 38 chains. Longest chain 9 peptides. Score 0.228 Round 2: 191 peptides, 34 chains. Longest chain 10 peptides. Score 0.338 Round 3: 196 peptides, 33 chains. Longest chain 12 peptides. Score 0.364 Round 4: 194 peptides, 30 chains. Longest chain 18 peptides. Score 0.394 Round 5: 187 peptides, 32 chains. Longest chain 18 peptides. Score 0.351 Taking the results from Round 4 Chains 30, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7488 restraints for refining 3341 atoms. 6862 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2926 (Rfree = 0.000) for 3341 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 32: After refmac, R = 0.2626 (Rfree = 0.000) for 3291 atoms. Found 15 (15 requested) and removed 28 (7 requested) atoms. Cycle 33: After refmac, R = 0.2665 (Rfree = 0.000) for 3255 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 34: After refmac, R = 0.2538 (Rfree = 0.000) for 3232 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 35: After refmac, R = 0.2509 (Rfree = 0.000) for 3201 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.94 3.74 Search for helices and strands: 0 residues in 0 chains, 3299 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3332 seeds are put forward Round 1: 132 peptides, 28 chains. Longest chain 9 peptides. Score 0.237 Round 2: 164 peptides, 30 chains. Longest chain 15 peptides. Score 0.310 Round 3: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.314 Round 4: 184 peptides, 31 chains. Longest chain 16 peptides. Score 0.355 Round 5: 184 peptides, 31 chains. Longest chain 14 peptides. Score 0.355 Taking the results from Round 5 Chains 31, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7695 restraints for refining 3300 atoms. 7114 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2791 (Rfree = 0.000) for 3300 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 37: After refmac, R = 0.2587 (Rfree = 0.000) for 3268 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 38: After refmac, R = 0.2428 (Rfree = 0.000) for 3247 atoms. Found 14 (15 requested) and removed 18 (7 requested) atoms. Cycle 39: After refmac, R = 0.2510 (Rfree = 0.000) for 3230 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 40: After refmac, R = 0.2268 (Rfree = 0.000) for 3210 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.01 3.80 Search for helices and strands: 0 residues in 0 chains, 3284 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3308 seeds are put forward Round 1: 144 peptides, 31 chains. Longest chain 8 peptides. Score 0.235 Round 2: 164 peptides, 31 chains. Longest chain 9 peptides. Score 0.297 Round 3: 173 peptides, 29 chains. Longest chain 13 peptides. Score 0.349 Round 4: 180 peptides, 29 chains. Longest chain 14 peptides. Score 0.369 Round 5: 172 peptides, 31 chains. Longest chain 16 peptides. Score 0.321 Taking the results from Round 4 Chains 29, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7405 restraints for refining 3250 atoms. 6830 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2455 (Rfree = 0.000) for 3250 atoms. Found 14 (15 requested) and removed 30 (7 requested) atoms. Cycle 42: After refmac, R = 0.2227 (Rfree = 0.000) for 3225 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 43: After refmac, R = 0.2034 (Rfree = 0.000) for 3211 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.1961 (Rfree = 0.000) for 3200 atoms. Found 3 (15 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.2085 (Rfree = 0.000) for 3184 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 3265 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3292 seeds are put forward Round 1: 157 peptides, 34 chains. Longest chain 10 peptides. Score 0.236 Round 2: 185 peptides, 35 chains. Longest chain 14 peptides. Score 0.308 Round 3: 179 peptides, 33 chains. Longest chain 10 peptides. Score 0.316 Round 4: 193 peptides, 35 chains. Longest chain 12 peptides. Score 0.331 Round 5: 193 peptides, 34 chains. Longest chain 14 peptides. Score 0.343 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 159, 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 2h1q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5367 reflections ( 99.54 % complete ) and 8171 restraints for refining 3459 atoms. 7569 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2652 (Rfree = 0.000) for 3459 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2578 (Rfree = 0.000) for 3435 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2485 (Rfree = 0.000) for 3400 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2544 (Rfree = 0.000) for 3376 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:29:34 GMT 2018 Job finished. TimeTaking 48.12 Used memory is bytes: 17670768