null Mon 24 Dec 07:45:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-noncs ############### 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 07:45:29 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/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-noncs/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 420 and 0 Target number of residues in the AU: 420 Target solvent content: 0.6268 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.2-parrot-noncs.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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.60 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: 29.850 3.200 Wilson plot Bfac: 64.58 10035 reflections ( 99.62 % complete ) and 0 restraints for refining 5969 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3132 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2381 (Rfree = 0.000) for 5969 atoms. Found 12 (53 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 6061 seeds are put forward NCS extension: 0 residues added, 6061 seeds are put forward Round 1: 246 peptides, 53 chains. Longest chain 8 peptides. Score 0.269 Round 2: 324 peptides, 56 chains. Longest chain 13 peptides. Score 0.444 Round 3: 354 peptides, 53 chains. Longest chain 20 peptides. Score 0.543 Round 4: 358 peptides, 53 chains. Longest chain 15 peptides. Score 0.551 Round 5: 345 peptides, 52 chains. Longest chain 13 peptides. Score 0.533 Taking the results from Round 4 Chains 53, Residues 305, Estimated correctness of the model 27.2 % 7 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10935 restraints for refining 4893 atoms. 9666 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2674 (Rfree = 0.000) for 4893 atoms. Found 41 (43 requested) and removed 26 (21 requested) atoms. Cycle 2: After refmac, R = 0.2390 (Rfree = 0.000) for 4874 atoms. Found 16 (44 requested) and removed 28 (22 requested) atoms. Cycle 3: After refmac, R = 0.2348 (Rfree = 0.000) for 4836 atoms. Found 10 (43 requested) and removed 21 (21 requested) atoms. Cycle 4: After refmac, R = 0.2304 (Rfree = 0.000) for 4819 atoms. Found 10 (43 requested) and removed 23 (21 requested) atoms. Cycle 5: After refmac, R = 0.2273 (Rfree = 0.000) for 4799 atoms. Found 6 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.70 Search for helices and strands: 0 residues in 0 chains, 4957 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4970 seeds are put forward Round 1: 312 peptides, 55 chains. Longest chain 16 peptides. Score 0.425 Round 2: 384 peptides, 56 chains. Longest chain 17 peptides. Score 0.577 Round 3: 398 peptides, 60 chains. Longest chain 14 peptides. Score 0.571 Round 4: 410 peptides, 58 chains. Longest chain 19 peptides. Score 0.611 Round 5: 390 peptides, 61 chains. Longest chain 19 peptides. Score 0.545 Taking the results from Round 4 Chains 62, Residues 352, Estimated correctness of the model 44.0 % 8 chains (52 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10122 restraints for refining 4728 atoms. 8620 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2661 (Rfree = 0.000) for 4728 atoms. Found 38 (42 requested) and removed 33 (21 requested) atoms. Cycle 7: After refmac, R = 0.2534 (Rfree = 0.000) for 4705 atoms. Found 16 (42 requested) and removed 30 (21 requested) atoms. Cycle 8: After refmac, R = 0.2476 (Rfree = 0.000) for 4672 atoms. Found 12 (42 requested) and removed 23 (21 requested) atoms. Cycle 9: After refmac, R = 0.2429 (Rfree = 0.000) for 4652 atoms. Found 3 (41 requested) and removed 22 (20 requested) atoms. Cycle 10: After refmac, R = 0.2395 (Rfree = 0.000) for 4628 atoms. Found 6 (41 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 4812 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4833 seeds are put forward Round 1: 326 peptides, 55 chains. Longest chain 13 peptides. Score 0.460 Round 2: 365 peptides, 54 chains. Longest chain 17 peptides. Score 0.556 Round 3: 348 peptides, 49 chains. Longest chain 21 peptides. Score 0.567 Round 4: 374 peptides, 51 chains. Longest chain 16 peptides. Score 0.601 Round 5: 383 peptides, 52 chains. Longest chain 24 peptides. Score 0.610 Taking the results from Round 5 Chains 52, Residues 331, Estimated correctness of the model 43.7 % 7 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10435 restraints for refining 4727 atoms. 9049 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2741 (Rfree = 0.000) for 4727 atoms. Found 42 (42 requested) and removed 34 (21 requested) atoms. Cycle 12: After refmac, R = 0.2521 (Rfree = 0.000) for 4732 atoms. Found 14 (42 requested) and removed 23 (21 requested) atoms. Cycle 13: After refmac, R = 0.2383 (Rfree = 0.000) for 4719 atoms. Found 6 (42 requested) and removed 21 (21 requested) atoms. Cycle 14: After refmac, R = 0.2322 (Rfree = 0.000) for 4696 atoms. Found 12 (42 requested) and removed 21 (21 requested) atoms. Cycle 15: After refmac, R = 0.2263 (Rfree = 0.000) for 4685 atoms. Found 6 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 4877 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 4900 seeds are put forward Round 1: 324 peptides, 56 chains. Longest chain 14 peptides. Score 0.444 Round 2: 355 peptides, 57 chains. Longest chain 16 peptides. Score 0.507 Round 3: 363 peptides, 53 chains. Longest chain 22 peptides. Score 0.561 Round 4: 358 peptides, 52 chains. Longest chain 21 peptides. Score 0.560 Round 5: 359 peptides, 56 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 3 Chains 53, Residues 310, Estimated correctness of the model 30.1 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10535 restraints for refining 4655 atoms. 9289 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2609 (Rfree = 0.000) for 4655 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 17: After refmac, R = 0.2428 (Rfree = 0.000) for 4666 atoms. Found 15 (41 requested) and removed 21 (20 requested) atoms. Cycle 18: After refmac, R = 0.2327 (Rfree = 0.000) for 4657 atoms. Found 6 (41 requested) and removed 20 (20 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 4640 atoms. Found 6 (41 requested) and removed 20 (20 requested) atoms. Cycle 20: After refmac, R = 0.2215 (Rfree = 0.000) for 4622 atoms. Found 8 (41 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4787 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 4813 seeds are put forward Round 1: 305 peptides, 55 chains. Longest chain 11 peptides. Score 0.408 Round 2: 354 peptides, 56 chains. Longest chain 15 peptides. Score 0.514 Round 3: 366 peptides, 54 chains. Longest chain 14 peptides. Score 0.559 Round 4: 372 peptides, 56 chains. Longest chain 16 peptides. Score 0.553 Round 5: 351 peptides, 54 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 3 Chains 55, Residues 312, Estimated correctness of the model 29.5 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10727 restraints for refining 4689 atoms. 9462 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2364 (Rfree = 0.000) for 4689 atoms. Found 22 (42 requested) and removed 27 (21 requested) atoms. Cycle 22: After refmac, R = 0.2228 (Rfree = 0.000) for 4673 atoms. Found 12 (42 requested) and removed 24 (21 requested) atoms. Cycle 23: After refmac, R = 0.2194 (Rfree = 0.000) for 4648 atoms. Found 12 (41 requested) and removed 24 (20 requested) atoms. Cycle 24: After refmac, R = 0.2199 (Rfree = 0.000) for 4632 atoms. Found 17 (41 requested) and removed 22 (20 requested) atoms. Cycle 25: After refmac, R = 0.2082 (Rfree = 0.000) for 4623 atoms. Found 7 (41 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4811 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4831 seeds are put forward Round 1: 289 peptides, 53 chains. Longest chain 10 peptides. Score 0.388 Round 2: 318 peptides, 51 chains. Longest chain 14 peptides. Score 0.481 Round 3: 320 peptides, 50 chains. Longest chain 14 peptides. Score 0.496 Round 4: 321 peptides, 46 chains. Longest chain 16 peptides. Score 0.537 Round 5: 318 peptides, 50 chains. Longest chain 16 peptides. Score 0.491 Taking the results from Round 4 Chains 46, Residues 275, Estimated correctness of the model 23.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10753 restraints for refining 4691 atoms. 9640 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2350 (Rfree = 0.000) for 4691 atoms. Found 35 (42 requested) and removed 28 (21 requested) atoms. Cycle 27: After refmac, R = 0.2169 (Rfree = 0.000) for 4690 atoms. Found 12 (42 requested) and removed 24 (21 requested) atoms. Cycle 28: After refmac, R = 0.2105 (Rfree = 0.000) for 4669 atoms. Found 12 (41 requested) and removed 21 (20 requested) atoms. Cycle 29: After refmac, R = 0.2084 (Rfree = 0.000) for 4656 atoms. Found 8 (41 requested) and removed 23 (20 requested) atoms. Cycle 30: After refmac, R = 0.2022 (Rfree = 0.000) for 4634 atoms. Found 6 (41 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4816 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4828 seeds are put forward Round 1: 251 peptides, 48 chains. Longest chain 9 peptides. Score 0.343 Round 2: 308 peptides, 46 chains. Longest chain 14 peptides. Score 0.509 Round 3: 305 peptides, 47 chains. Longest chain 14 peptides. Score 0.492 Round 4: 313 peptides, 50 chains. Longest chain 13 peptides. Score 0.480 Round 5: 313 peptides, 49 chains. Longest chain 12 peptides. Score 0.490 Taking the results from Round 2 Chains 46, Residues 262, Estimated correctness of the model 14.2 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10801 restraints for refining 4656 atoms. 9742 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2209 (Rfree = 0.000) for 4656 atoms. Found 36 (41 requested) and removed 28 (20 requested) atoms. Cycle 32: After refmac, R = 0.2043 (Rfree = 0.000) for 4662 atoms. Found 13 (41 requested) and removed 21 (20 requested) atoms. Cycle 33: After refmac, R = 0.1966 (Rfree = 0.000) for 4650 atoms. Found 7 (41 requested) and removed 23 (20 requested) atoms. Cycle 34: After refmac, R = 0.1962 (Rfree = 0.000) for 4627 atoms. Found 5 (41 requested) and removed 20 (20 requested) atoms. Cycle 35: After refmac, R = 0.2039 (Rfree = 0.000) for 4606 atoms. Found 17 (41 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.61 Search for helices and strands: 0 residues in 0 chains, 4797 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 4809 seeds are put forward Round 1: 275 peptides, 54 chains. Longest chain 9 peptides. Score 0.339 Round 2: 310 peptides, 47 chains. Longest chain 21 peptides. Score 0.503 Round 3: 333 peptides, 50 chains. Longest chain 22 peptides. Score 0.525 Round 4: 328 peptides, 47 chains. Longest chain 16 peptides. Score 0.543 Round 5: 297 peptides, 44 chains. Longest chain 15 peptides. Score 0.503 Taking the results from Round 4 Chains 48, Residues 281, Estimated correctness of the model 24.8 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10771 restraints for refining 4716 atoms. 9629 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2319 (Rfree = 0.000) for 4716 atoms. Found 37 (42 requested) and removed 31 (21 requested) atoms. Cycle 37: After refmac, R = 0.2159 (Rfree = 0.000) for 4720 atoms. Found 12 (42 requested) and removed 24 (21 requested) atoms. Cycle 38: After refmac, R = 0.2077 (Rfree = 0.000) for 4698 atoms. Found 11 (42 requested) and removed 23 (21 requested) atoms. Cycle 39: After refmac, R = 0.2046 (Rfree = 0.000) for 4684 atoms. Found 7 (42 requested) and removed 22 (21 requested) atoms. Cycle 40: After refmac, R = 0.2041 (Rfree = 0.000) for 4668 atoms. Found 9 (41 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 4847 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 4862 seeds are put forward Round 1: 239 peptides, 46 chains. Longest chain 14 peptides. Score 0.333 Round 2: 318 peptides, 46 chains. Longest chain 17 peptides. Score 0.531 Round 3: 319 peptides, 48 chains. Longest chain 17 peptides. Score 0.514 Round 4: 328 peptides, 48 chains. Longest chain 17 peptides. Score 0.534 Round 5: 302 peptides, 44 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 4 Chains 50, Residues 280, Estimated correctness of the model 22.1 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10809 restraints for refining 4796 atoms. 9614 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2495 (Rfree = 0.000) for 4796 atoms. Found 42 (43 requested) and removed 37 (21 requested) atoms. Cycle 42: After refmac, R = 0.2198 (Rfree = 0.000) for 4795 atoms. Found 14 (43 requested) and removed 21 (21 requested) atoms. Cycle 43: After refmac, R = 0.2100 (Rfree = 0.000) for 4781 atoms. Found 10 (42 requested) and removed 21 (21 requested) atoms. Cycle 44: After refmac, R = 0.2069 (Rfree = 0.000) for 4766 atoms. Found 7 (42 requested) and removed 21 (21 requested) atoms. Cycle 45: After refmac, R = 0.2079 (Rfree = 0.000) for 4750 atoms. Found 6 (42 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 4949 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4978 seeds are put forward Round 1: 246 peptides, 44 chains. Longest chain 13 peptides. Score 0.376 Round 2: 276 peptides, 43 chains. Longest chain 18 peptides. Score 0.464 Round 3: 274 peptides, 42 chains. Longest chain 16 peptides. Score 0.470 Round 4: 268 peptides, 44 chains. Longest chain 11 peptides. Score 0.433 Round 5: 282 peptides, 41 chains. Longest chain 18 peptides. Score 0.499 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 241, Estimated correctness of the model 11.0 % 3 chains (19 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 213 A and 223 A 40 chains (246 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10035 reflections ( 99.62 % complete ) and 11096 restraints for refining 4814 atoms. 10067 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2511 (Rfree = 0.000) for 4814 atoms. Found 0 (43 requested) and removed 9 (21 requested) atoms. Cycle 47: After refmac, R = 0.2371 (Rfree = 0.000) for 4799 atoms. Found 0 (43 requested) and removed 9 (21 requested) atoms. Cycle 48: After refmac, R = 0.2292 (Rfree = 0.000) for 4789 atoms. Found 0 (42 requested) and removed 4 (21 requested) atoms. Cycle 49: After refmac, R = 0.2197 (Rfree = 0.000) for 4783 atoms. Found 0 (42 requested) and removed 13 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:34:30 GMT 2018 Job finished. TimeTaking 49.1 Used memory is bytes: 6826024