null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hxv-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-3.6-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-3.6-parrot-hancs/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 262 and 0 Target number of residues in the AU: 262 Target solvent content: 0.6441 Checking the provided sequence file Detected sequence length: 360 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 360 Adjusted target solvent content: 0.51 Input MTZ file: 2hxv-3.6-parrot-hancs.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: 97 Cell parameters: 104.410 104.410 146.200 90.000 90.000 90.000 Input sequence file: 2hxv-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2880 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 Loops will be built when appropriate and at the last cycle Resolution range: 84.967 3.600 Wilson plot Bfac: 74.44 4928 reflections ( 99.44 % complete ) and 0 restraints for refining 3200 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3403 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 3200 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward Round 1: 127 peptides, 25 chains. Longest chain 8 peptides. Score 0.298 Round 2: 175 peptides, 29 chains. Longest chain 17 peptides. Score 0.428 Round 3: 201 peptides, 32 chains. Longest chain 17 peptides. Score 0.477 Round 4: 208 peptides, 31 chains. Longest chain 15 peptides. Score 0.517 Round 5: 217 peptides, 30 chains. Longest chain 21 peptides. Score 0.561 Taking the results from Round 5 Chains 30, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5954 restraints for refining 2593 atoms. 5236 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3050 (Rfree = 0.000) for 2593 atoms. Found 15 (16 requested) and removed 45 (8 requested) atoms. Cycle 2: After refmac, R = 0.2947 (Rfree = 0.000) for 2509 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2874 (Rfree = 0.000) for 2475 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 4: After refmac, R = 0.2824 (Rfree = 0.000) for 2460 atoms. Found 13 (15 requested) and removed 20 (7 requested) atoms. Cycle 5: After refmac, R = 0.2724 (Rfree = 0.000) for 2442 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 2534 seeds are put forward Round 1: 177 peptides, 34 chains. Longest chain 10 peptides. Score 0.350 Round 2: 206 peptides, 29 chains. Longest chain 20 peptides. Score 0.540 Round 3: 223 peptides, 33 chains. Longest chain 32 peptides. Score 0.538 Round 4: 209 peptides, 29 chains. Longest chain 20 peptides. Score 0.550 Round 5: 211 peptides, 30 chains. Longest chain 32 peptides. Score 0.542 Taking the results from Round 4 Chains 30, Residues 180, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5562 restraints for refining 2534 atoms. 4813 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2723 (Rfree = 0.000) for 2534 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 7: After refmac, R = 0.2457 (Rfree = 0.000) for 2511 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2460 (Rfree = 0.000) for 2489 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 9: After refmac, R = 0.2314 (Rfree = 0.000) for 2475 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2308 (Rfree = 0.000) for 2463 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 2573 seeds are put forward Round 1: 191 peptides, 35 chains. Longest chain 13 peptides. Score 0.390 Round 2: 218 peptides, 33 chains. Longest chain 20 peptides. Score 0.521 Round 3: 218 peptides, 31 chains. Longest chain 18 peptides. Score 0.550 Round 4: 214 peptides, 27 chains. Longest chain 24 peptides. Score 0.594 Round 5: 213 peptides, 27 chains. Longest chain 22 peptides. Score 0.590 Taking the results from Round 4 Chains 29, Residues 187, Estimated correctness of the model 12.3 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5458 restraints for refining 2609 atoms. 4582 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2879 (Rfree = 0.000) for 2609 atoms. Found 16 (16 requested) and removed 55 (8 requested) atoms. Cycle 12: After refmac, R = 0.2755 (Rfree = 0.000) for 2546 atoms. Found 15 (16 requested) and removed 21 (8 requested) atoms. Cycle 13: After refmac, R = 0.2522 (Rfree = 0.000) for 2513 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2478 (Rfree = 0.000) for 2509 atoms. Found 13 (16 requested) and removed 23 (8 requested) atoms. Cycle 15: After refmac, R = 0.2379 (Rfree = 0.000) for 2495 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 2558 seeds are put forward Round 1: 177 peptides, 32 chains. Longest chain 16 peptides. Score 0.385 Round 2: 196 peptides, 26 chains. Longest chain 19 peptides. Score 0.551 Round 3: 204 peptides, 30 chains. Longest chain 15 peptides. Score 0.518 Round 4: 196 peptides, 26 chains. Longest chain 20 peptides. Score 0.551 Round 5: 200 peptides, 28 chains. Longest chain 24 peptides. Score 0.534 Taking the results from Round 4 Chains 28, Residues 170, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5766 restraints for refining 2610 atoms. 5016 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2786 (Rfree = 0.000) for 2610 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 17: After refmac, R = 0.2497 (Rfree = 0.000) for 2581 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.2505 (Rfree = 0.000) for 2570 atoms. Found 15 (16 requested) and removed 16 (8 requested) atoms. Cycle 19: After refmac, R = 0.2100 (Rfree = 0.000) for 2557 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2301 (Rfree = 0.000) for 2548 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 2617 seeds are put forward Round 1: 162 peptides, 31 chains. Longest chain 10 peptides. Score 0.340 Round 2: 192 peptides, 31 chains. Longest chain 24 peptides. Score 0.460 Round 3: 202 peptides, 31 chains. Longest chain 20 peptides. Score 0.496 Round 4: 208 peptides, 25 chains. Longest chain 24 peptides. Score 0.603 Round 5: 205 peptides, 27 chains. Longest chain 20 peptides. Score 0.565 Taking the results from Round 4 Chains 28, Residues 183, Estimated correctness of the model 15.8 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5535 restraints for refining 2609 atoms. 4744 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2561 (Rfree = 0.000) for 2609 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. Cycle 22: After refmac, R = 0.2352 (Rfree = 0.000) for 2593 atoms. Found 10 (16 requested) and removed 18 (8 requested) atoms. Cycle 23: After refmac, R = 0.2350 (Rfree = 0.000) for 2576 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 24: After refmac, R = 0.2285 (Rfree = 0.000) for 2567 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 25: After refmac, R = 0.2270 (Rfree = 0.000) for 2558 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 2645 seeds are put forward Round 1: 159 peptides, 29 chains. Longest chain 17 peptides. Score 0.364 Round 2: 180 peptides, 25 chains. Longest chain 28 peptides. Score 0.512 Round 3: 174 peptides, 27 chains. Longest chain 12 peptides. Score 0.458 Round 4: 172 peptides, 25 chains. Longest chain 23 peptides. Score 0.483 Round 5: 169 peptides, 25 chains. Longest chain 21 peptides. Score 0.472 Taking the results from Round 2 Chains 27, Residues 155, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5777 restraints for refining 2610 atoms. 5146 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2384 (Rfree = 0.000) for 2610 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.2291 (Rfree = 0.000) for 2598 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2346 (Rfree = 0.000) for 2590 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.2087 (Rfree = 0.000) for 2589 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.2039 (Rfree = 0.000) for 2591 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 2675 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 11 peptides. Score 0.314 Round 2: 182 peptides, 28 chains. Longest chain 18 peptides. Score 0.471 Round 3: 184 peptides, 30 chains. Longest chain 15 peptides. Score 0.446 Round 4: 189 peptides, 25 chains. Longest chain 24 peptides. Score 0.543 Round 5: 195 peptides, 31 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 4 Chains 25, Residues 164, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5695 restraints for refining 2610 atoms. 4981 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2475 (Rfree = 0.000) for 2610 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.2308 (Rfree = 0.000) for 2600 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 2584 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.2229 (Rfree = 0.000) for 2582 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2118 (Rfree = 0.000) for 2582 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 2675 seeds are put forward Round 1: 124 peptides, 25 chains. Longest chain 10 peptides. Score 0.285 Round 2: 135 peptides, 24 chains. Longest chain 14 peptides. Score 0.353 Round 3: 137 peptides, 24 chains. Longest chain 14 peptides. Score 0.362 Round 4: 155 peptides, 22 chains. Longest chain 16 peptides. Score 0.470 Round 5: 152 peptides, 25 chains. Longest chain 19 peptides. Score 0.406 Taking the results from Round 4 Chains 23, Residues 133, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 6045 restraints for refining 2610 atoms. 5488 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2329 (Rfree = 0.000) for 2610 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 37: After refmac, R = 0.2304 (Rfree = 0.000) for 2595 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.2244 (Rfree = 0.000) for 2593 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2395 (Rfree = 0.000) for 2588 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.2428 (Rfree = 0.000) for 2581 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 2650 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 8 peptides. Score 0.250 Round 2: 145 peptides, 28 chains. Longest chain 9 peptides. Score 0.322 Round 3: 142 peptides, 26 chains. Longest chain 14 peptides. Score 0.346 Round 4: 147 peptides, 22 chains. Longest chain 12 peptides. Score 0.439 Round 5: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.367 Taking the results from Round 4 Chains 22, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4928 reflections ( 99.44 % complete ) and 5985 restraints for refining 2609 atoms. 5507 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2731 (Rfree = 0.000) for 2609 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 42: After refmac, R = 0.2588 (Rfree = 0.000) for 2585 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 43: After refmac, R = 0.2662 (Rfree = 0.000) for 2574 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2470 (Rfree = 0.000) for 2572 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 45: After refmac, R = 0.2382 (Rfree = 0.000) for 2569 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 2627 seeds are put forward Round 1: 102 peptides, 23 chains. Longest chain 7 peptides. Score 0.219 Round 2: 111 peptides, 21 chains. Longest chain 9 peptides. Score 0.304 Round 3: 119 peptides, 24 chains. Longest chain 8 peptides. Score 0.281 Round 4: 121 peptides, 20 chains. Longest chain 9 peptides. Score 0.368 Round 5: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.327 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 101, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2hxv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4928 reflections ( 99.44 % complete ) and 5857 restraints for refining 2552 atoms. 5459 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2704 (Rfree = 0.000) for 2552 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2428 (Rfree = 0.000) for 2532 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2030 (Rfree = 0.000) for 2521 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1942 (Rfree = 0.000) for 2511 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:21:31 GMT 2018 Job finished. TimeTaking 53.57 Used memory is bytes: 12160088