null Mon 24 Dec 07:26:54 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 2otm-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-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/2otm-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-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 07:26:58 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/2otm-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6127 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3696 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: 78.536 3.200 Wilson plot Bfac: 57.84 9162 reflections ( 99.84 % complete ) and 0 restraints for refining 4070 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3104 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2632 (Rfree = 0.000) for 4070 atoms. Found 32 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.88 Search for helices and strands: 0 residues in 0 chains, 4149 seeds are put forward NCS extension: 0 residues added, 4149 seeds are put forward Round 1: 241 peptides, 43 chains. Longest chain 19 peptides. Score 0.389 Round 2: 305 peptides, 42 chains. Longest chain 21 peptides. Score 0.566 Round 3: 323 peptides, 38 chains. Longest chain 33 peptides. Score 0.642 Round 4: 341 peptides, 39 chains. Longest chain 30 peptides. Score 0.668 Round 5: 358 peptides, 27 chains. Longest chain 41 peptides. Score 0.782 Taking the results from Round 5 Chains 36, Residues 331, Estimated correctness of the model 80.6 % 9 chains (166 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 B and 27 B 35 chains (336 residues) following loop building 8 chains (174 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5377 restraints for refining 3424 atoms. 3423 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2743 (Rfree = 0.000) for 3424 atoms. Found 27 (30 requested) and removed 35 (15 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 3364 atoms. Found 10 (29 requested) and removed 23 (15 requested) atoms. Cycle 3: After refmac, R = 0.2412 (Rfree = 0.000) for 3321 atoms. Found 12 (29 requested) and removed 22 (15 requested) atoms. Cycle 4: After refmac, R = 0.2495 (Rfree = 0.000) for 3295 atoms. Found 18 (27 requested) and removed 22 (14 requested) atoms. Cycle 5: After refmac, R = 0.2199 (Rfree = 0.000) for 3265 atoms. Found 6 (27 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 3347 seeds are put forward NCS extension: 38 residues added (24 deleted due to clashes), 3385 seeds are put forward Round 1: 342 peptides, 34 chains. Longest chain 27 peptides. Score 0.710 Round 2: 362 peptides, 28 chains. Longest chain 45 peptides. Score 0.781 Round 3: 359 peptides, 35 chains. Longest chain 42 peptides. Score 0.729 Round 4: 362 peptides, 30 chains. Longest chain 42 peptides. Score 0.768 Round 5: 361 peptides, 28 chains. Longest chain 35 peptides. Score 0.780 Taking the results from Round 2 Chains 30, Residues 334, Estimated correctness of the model 80.4 % 6 chains (125 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 27 A 29 chains (343 residues) following loop building 5 chains (135 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5778 restraints for refining 3373 atoms. 3946 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2656 (Rfree = 0.000) for 3373 atoms. Found 27 (27 requested) and removed 32 (15 requested) atoms. Cycle 7: After refmac, R = 0.2337 (Rfree = 0.000) for 3346 atoms. Found 9 (26 requested) and removed 17 (15 requested) atoms. Cycle 8: After refmac, R = 0.2235 (Rfree = 0.000) for 3325 atoms. Found 8 (25 requested) and removed 15 (14 requested) atoms. Cycle 9: After refmac, R = 0.2168 (Rfree = 0.000) for 3315 atoms. Found 4 (24 requested) and removed 14 (14 requested) atoms. Cycle 10: After refmac, R = 0.2113 (Rfree = 0.000) for 3302 atoms. Found 2 (24 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 2.82 Search for helices and strands: 0 residues in 0 chains, 3374 seeds are put forward NCS extension: 90 residues added (35 deleted due to clashes), 3464 seeds are put forward Round 1: 336 peptides, 30 chains. Longest chain 40 peptides. Score 0.731 Round 2: 360 peptides, 32 chains. Longest chain 40 peptides. Score 0.752 Round 3: 371 peptides, 32 chains. Longest chain 36 peptides. Score 0.767 Round 4: 361 peptides, 27 chains. Longest chain 42 peptides. Score 0.786 Round 5: 361 peptides, 35 chains. Longest chain 25 peptides. Score 0.732 Taking the results from Round 4 Chains 29, Residues 334, Estimated correctness of the model 81.2 % 4 chains (94 residues) have been docked in sequence Building loops using Loopy2018 29 chains (334 residues) following loop building 4 chains (94 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6108 restraints for refining 3375 atoms. 4423 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2515 (Rfree = 0.000) for 3375 atoms. Found 20 (24 requested) and removed 20 (15 requested) atoms. Cycle 12: After refmac, R = 0.2380 (Rfree = 0.000) for 3368 atoms. Found 9 (23 requested) and removed 19 (15 requested) atoms. Cycle 13: After refmac, R = 0.2274 (Rfree = 0.000) for 3354 atoms. Found 8 (23 requested) and removed 22 (15 requested) atoms. Cycle 14: After refmac, R = 0.2165 (Rfree = 0.000) for 3334 atoms. Found 5 (21 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.2121 (Rfree = 0.000) for 3322 atoms. Found 8 (21 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 2.84 Search for helices and strands: 0 residues in 0 chains, 3414 seeds are put forward NCS extension: 30 residues added (23 deleted due to clashes), 3444 seeds are put forward Round 1: 340 peptides, 34 chains. Longest chain 28 peptides. Score 0.706 Round 2: 371 peptides, 33 chains. Longest chain 36 peptides. Score 0.761 Round 3: 366 peptides, 29 chains. Longest chain 43 peptides. Score 0.780 Round 4: 344 peptides, 32 chains. Longest chain 42 peptides. Score 0.728 Round 5: 360 peptides, 32 chains. Longest chain 33 peptides. Score 0.752 Taking the results from Round 3 Chains 35, Residues 337, Estimated correctness of the model 80.3 % 7 chains (116 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A 34 chains (338 residues) following loop building 6 chains (118 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5946 restraints for refining 3373 atoms. 4217 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2469 (Rfree = 0.000) for 3373 atoms. Found 21 (21 requested) and removed 24 (15 requested) atoms. Cycle 17: After refmac, R = 0.2666 (Rfree = 0.000) for 3359 atoms. Found 20 (20 requested) and removed 32 (15 requested) atoms. Cycle 18: After refmac, R = 0.2280 (Rfree = 0.000) for 3333 atoms. Found 10 (20 requested) and removed 21 (15 requested) atoms. Cycle 19: After refmac, R = 0.2232 (Rfree = 0.000) for 3317 atoms. Found 10 (19 requested) and removed 19 (14 requested) atoms. Cycle 20: After refmac, R = 0.2145 (Rfree = 0.000) for 3304 atoms. Found 4 (18 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 3380 seeds are put forward NCS extension: 13 residues added (14 deleted due to clashes), 3393 seeds are put forward Round 1: 327 peptides, 35 chains. Longest chain 28 peptides. Score 0.676 Round 2: 352 peptides, 31 chains. Longest chain 43 peptides. Score 0.747 Round 3: 353 peptides, 31 chains. Longest chain 42 peptides. Score 0.749 Round 4: 341 peptides, 30 chains. Longest chain 33 peptides. Score 0.738 Round 5: 342 peptides, 28 chains. Longest chain 42 peptides. Score 0.754 Taking the results from Round 5 Chains 36, Residues 314, Estimated correctness of the model 75.8 % 9 chains (165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 50 A Built loop between residues 44 C and 48 C 32 chains (317 residues) following loop building 7 chains (171 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5360 restraints for refining 3375 atoms. 3424 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2601 (Rfree = 0.000) for 3375 atoms. Found 18 (18 requested) and removed 36 (15 requested) atoms. Cycle 22: After refmac, R = 0.2696 (Rfree = 0.000) for 3347 atoms. Found 17 (17 requested) and removed 32 (15 requested) atoms. Cycle 23: After refmac, R = 0.2546 (Rfree = 0.000) for 3316 atoms. Found 16 (16 requested) and removed 26 (14 requested) atoms. Cycle 24: After refmac, R = 0.2445 (Rfree = 0.000) for 3295 atoms. Found 16 (16 requested) and removed 25 (14 requested) atoms. Cycle 25: After refmac, R = 0.2485 (Rfree = 0.000) for 3273 atoms. Found 15 (15 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 2.82 Search for helices and strands: 0 residues in 0 chains, 3339 seeds are put forward NCS extension: 15 residues added (10 deleted due to clashes), 3354 seeds are put forward Round 1: 308 peptides, 35 chains. Longest chain 33 peptides. Score 0.640 Round 2: 337 peptides, 37 chains. Longest chain 28 peptides. Score 0.677 Round 3: 340 peptides, 34 chains. Longest chain 36 peptides. Score 0.706 Round 4: 348 peptides, 27 chains. Longest chain 45 peptides. Score 0.769 Round 5: 344 peptides, 35 chains. Longest chain 37 peptides. Score 0.705 Taking the results from Round 4 Chains 32, Residues 321, Estimated correctness of the model 78.4 % 10 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 50 A 31 chains (323 residues) following loop building 9 chains (165 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5450 restraints for refining 3375 atoms. 3582 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2510 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 23 (15 requested) atoms. Cycle 27: After refmac, R = 0.2573 (Rfree = 0.000) for 3356 atoms. Found 15 (15 requested) and removed 25 (15 requested) atoms. Cycle 28: After refmac, R = 0.2581 (Rfree = 0.000) for 3338 atoms. Found 15 (15 requested) and removed 28 (15 requested) atoms. Cycle 29: After refmac, R = 0.2154 (Rfree = 0.000) for 3318 atoms. Found 10 (14 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2529 (Rfree = 0.000) for 3310 atoms. Found 14 (14 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 2.82 Search for helices and strands: 0 residues in 0 chains, 3390 seeds are put forward NCS extension: 22 residues added (14 deleted due to clashes), 3412 seeds are put forward Round 1: 311 peptides, 36 chains. Longest chain 29 peptides. Score 0.637 Round 2: 332 peptides, 36 chains. Longest chain 35 peptides. Score 0.676 Round 3: 328 peptides, 33 chains. Longest chain 30 peptides. Score 0.694 Round 4: 321 peptides, 35 chains. Longest chain 23 peptides. Score 0.665 Round 5: 313 peptides, 34 chains. Longest chain 30 peptides. Score 0.658 Taking the results from Round 3 Chains 37, Residues 295, Estimated correctness of the model 63.9 % 9 chains (125 residues) have been docked in sequence ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6040 restraints for refining 3375 atoms. 4402 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2494 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 24 (15 requested) atoms. Cycle 32: After refmac, R = 0.2214 (Rfree = 0.000) for 3355 atoms. Found 10 (15 requested) and removed 22 (15 requested) atoms. Cycle 33: After refmac, R = 0.2203 (Rfree = 0.000) for 3339 atoms. Found 13 (15 requested) and removed 20 (15 requested) atoms. Cycle 34: After refmac, R = 0.1972 (Rfree = 0.000) for 3329 atoms. Found 8 (14 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.2144 (Rfree = 0.000) for 3321 atoms. Found 14 (14 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 2.85 Search for helices and strands: 0 residues in 0 chains, 3408 seeds are put forward NCS extension: 12 residues added (12 deleted due to clashes), 3420 seeds are put forward Round 1: 308 peptides, 35 chains. Longest chain 35 peptides. Score 0.640 Round 2: 330 peptides, 31 chains. Longest chain 39 peptides. Score 0.713 Round 3: 323 peptides, 33 chains. Longest chain 40 peptides. Score 0.685 Round 4: 346 peptides, 34 chains. Longest chain 26 peptides. Score 0.716 Round 5: 340 peptides, 35 chains. Longest chain 35 peptides. Score 0.699 Taking the results from Round 4 Chains 35, Residues 312, Estimated correctness of the model 68.5 % 7 chains (98 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 52 B 33 chains (315 residues) following loop building 6 chains (103 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6181 restraints for refining 3375 atoms. 4563 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2438 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 26 (15 requested) atoms. Cycle 37: After refmac, R = 0.2437 (Rfree = 0.000) for 3355 atoms. Found 15 (15 requested) and removed 20 (15 requested) atoms. Cycle 38: After refmac, R = 0.2483 (Rfree = 0.000) for 3341 atoms. Found 15 (15 requested) and removed 20 (15 requested) atoms. Cycle 39: After refmac, R = 0.2047 (Rfree = 0.000) for 3329 atoms. Found 9 (14 requested) and removed 16 (14 requested) atoms. Cycle 40: After refmac, R = 0.1994 (Rfree = 0.000) for 3318 atoms. Found 8 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 2.87 Search for helices and strands: 0 residues in 0 chains, 3419 seeds are put forward NCS extension: 32 residues added (10 deleted due to clashes), 3451 seeds are put forward Round 1: 288 peptides, 36 chains. Longest chain 38 peptides. Score 0.588 Round 2: 306 peptides, 34 chains. Longest chain 35 peptides. Score 0.645 Round 3: 314 peptides, 30 chains. Longest chain 51 peptides. Score 0.694 Round 4: 334 peptides, 34 chains. Longest chain 51 peptides. Score 0.696 Round 5: 335 peptides, 30 chains. Longest chain 29 peptides. Score 0.729 Taking the results from Round 5 Chains 34, Residues 305, Estimated correctness of the model 71.1 % 7 chains (90 residues) have been docked in sequence Building loops using Loopy2018 34 chains (305 residues) following loop building 7 chains (90 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6321 restraints for refining 3375 atoms. 4796 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2738 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 31 (15 requested) atoms. Cycle 42: After refmac, R = 0.2619 (Rfree = 0.000) for 3352 atoms. Found 15 (15 requested) and removed 24 (15 requested) atoms. Cycle 43: After refmac, R = 0.2206 (Rfree = 0.000) for 3333 atoms. Found 14 (15 requested) and removed 18 (15 requested) atoms. Cycle 44: After refmac, R = 0.2091 (Rfree = 0.000) for 3324 atoms. Found 6 (14 requested) and removed 16 (14 requested) atoms. Cycle 45: After refmac, R = 0.2082 (Rfree = 0.000) for 3311 atoms. Found 8 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 2.88 Search for helices and strands: 0 residues in 0 chains, 3393 seeds are put forward NCS extension: 24 residues added (18 deleted due to clashes), 3417 seeds are put forward Round 1: 305 peptides, 35 chains. Longest chain 37 peptides. Score 0.634 Round 2: 333 peptides, 30 chains. Longest chain 29 peptides. Score 0.726 Round 3: 330 peptides, 35 chains. Longest chain 40 peptides. Score 0.681 Round 4: 321 peptides, 30 chains. Longest chain 28 peptides. Score 0.706 Round 5: 302 peptides, 32 chains. Longest chain 30 peptides. Score 0.655 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 303, Estimated correctness of the model 70.5 % 6 chains (94 residues) have been docked in sequence Sequence coverage is 30 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (303 residues) following loop building 6 chains (94 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9162 reflections ( 99.84 % complete ) and 6231 restraints for refining 3375 atoms. 4681 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2345 (Rfree = 0.000) for 3375 atoms. Found 0 (15 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2127 (Rfree = 0.000) for 3352 atoms. Found 0 (15 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2059 (Rfree = 0.000) for 3333 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2042 (Rfree = 0.000) for 3315 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:12:47 GMT 2018 Job finished. TimeTaking 45.89 Used memory is bytes: 14558568