null Mon 24 Dec 01:00:57 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 2avn-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-2.5-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/2avn-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-2.5-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 01:01:02 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/2avn-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-2.5-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 763 and 0 Target number of residues in the AU: 763 Target solvent content: 0.5762 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 520 Adjusted target solvent content: 0.71 Input MTZ file: 2avn-2.5-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.05 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: 115.845 2.500 Wilson plot Bfac: 43.67 35104 reflections ( 99.87 % complete ) and 0 restraints for refining 4678 atoms. Observations/parameters ratio is 1.88 ------------------------------------------------------ Starting model: R = 0.3537 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2987 (Rfree = 0.000) for 4678 atoms. Found 84 (84 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.80 2.08 NCS extension: 0 residues added, 4718 seeds are put forward Round 1: 397 peptides, 39 chains. Longest chain 30 peptides. Score 0.592 Round 2: 442 peptides, 33 chains. Longest chain 41 peptides. Score 0.680 Round 3: 447 peptides, 23 chains. Longest chain 51 peptides. Score 0.736 Round 4: 455 peptides, 25 chains. Longest chain 54 peptides. Score 0.733 Round 5: 465 peptides, 26 chains. Longest chain 46 peptides. Score 0.738 Taking the results from Round 5 Chains 29, Residues 439, Estimated correctness of the model 87.6 % 14 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 99 A Built loop between residues 143 A and 146 A Built loop between residues 63 B and 72 B Built loop between residues 89 B and 92 B Built loop between residues 106 B and 115 B Built loop between residues 198 B and 201 B 20 chains (454 residues) following loop building 8 chains (376 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 5445 restraints for refining 4409 atoms. 2030 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3073 (Rfree = 0.000) for 4409 atoms. Found 80 (80 requested) and removed 55 (40 requested) atoms. Cycle 2: After refmac, R = 0.2806 (Rfree = 0.000) for 4373 atoms. Found 78 (78 requested) and removed 49 (40 requested) atoms. Cycle 3: After refmac, R = 0.2618 (Rfree = 0.000) for 4364 atoms. Found 76 (76 requested) and removed 49 (39 requested) atoms. Cycle 4: After refmac, R = 0.2446 (Rfree = 0.000) for 4378 atoms. Found 74 (74 requested) and removed 43 (39 requested) atoms. Cycle 5: After refmac, R = 0.2325 (Rfree = 0.000) for 4395 atoms. Found 73 (73 requested) and removed 42 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.61 1.94 NCS extension: 29 residues added (56 deleted due to clashes), 4473 seeds are put forward Round 1: 470 peptides, 19 chains. Longest chain 71 peptides. Score 0.774 Round 2: 486 peptides, 9 chains. Longest chain 163 peptides. Score 0.827 Round 3: 477 peptides, 14 chains. Longest chain 98 peptides. Score 0.801 Round 4: 484 peptides, 10 chains. Longest chain 121 peptides. Score 0.822 Round 5: 476 peptides, 17 chains. Longest chain 70 peptides. Score 0.787 Taking the results from Round 2 Chains 9, Residues 477, Estimated correctness of the model 94.2 % 8 chains (474 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 70 A Built loop between residues 168 A and 171 A Built loop between residues 222 A and 227 A Built loop between residues 41 B and 44 B Built loop between residues 54 B and 57 B Built loop between residues 218 B and 221 B 2 chains (493 residues) following loop building 2 chains (493 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4564 restraints for refining 4536 atoms. 411 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2285 (Rfree = 0.000) for 4536 atoms. Found 74 (74 requested) and removed 65 (41 requested) atoms. Cycle 7: After refmac, R = 0.2053 (Rfree = 0.000) for 4518 atoms. Found 72 (72 requested) and removed 43 (41 requested) atoms. Cycle 8: After refmac, R = 0.1950 (Rfree = 0.000) for 4535 atoms. Found 71 (71 requested) and removed 45 (41 requested) atoms. Cycle 9: After refmac, R = 0.1881 (Rfree = 0.000) for 4555 atoms. Found 69 (69 requested) and removed 46 (41 requested) atoms. Cycle 10: After refmac, R = 0.1835 (Rfree = 0.000) for 4570 atoms. Found 68 (68 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.59 1.92 NCS extension: 7 residues added (26 deleted due to clashes), 4613 seeds are put forward Round 1: 486 peptides, 6 chains. Longest chain 171 peptides. Score 0.838 Round 2: 484 peptides, 9 chains. Longest chain 104 peptides. Score 0.826 Round 3: 483 peptides, 8 chains. Longest chain 126 peptides. Score 0.829 Round 4: 478 peptides, 13 chains. Longest chain 94 peptides. Score 0.805 Round 5: 478 peptides, 15 chains. Longest chain 114 peptides. Score 0.797 Taking the results from Round 1 Chains 9, Residues 480, Estimated correctness of the model 94.8 % 7 chains (474 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 107 A Built loop between residues 181 A and 185 A Built loop between residues 226 A and 229 A Built loop between residues 60 B and 63 B Built loop between residues 182 B and 185 B 2 chains (489 residues) following loop building 2 chains (489 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4534 restraints for refining 4480 atoms. 421 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1973 (Rfree = 0.000) for 4480 atoms. Found 65 (65 requested) and removed 51 (40 requested) atoms. Cycle 12: After refmac, R = 0.1812 (Rfree = 0.000) for 4484 atoms. Found 63 (63 requested) and removed 45 (40 requested) atoms. Cycle 13: After refmac, R = 0.1758 (Rfree = 0.000) for 4499 atoms. Found 62 (62 requested) and removed 42 (40 requested) atoms. Cycle 14: After refmac, R = 0.1718 (Rfree = 0.000) for 4514 atoms. Found 60 (60 requested) and removed 42 (40 requested) atoms. Cycle 15: After refmac, R = 0.1684 (Rfree = 0.000) for 4528 atoms. Found 59 (59 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added, 4544 seeds are put forward Round 1: 489 peptides, 6 chains. Longest chain 171 peptides. Score 0.840 Round 2: 489 peptides, 7 chains. Longest chain 132 peptides. Score 0.836 Round 3: 484 peptides, 9 chains. Longest chain 140 peptides. Score 0.826 Round 4: 476 peptides, 15 chains. Longest chain 80 peptides. Score 0.796 Round 5: 482 peptides, 13 chains. Longest chain 93 peptides. Score 0.808 Taking the results from Round 1 Chains 6, Residues 483, Estimated correctness of the model 95.0 % 6 chains (483 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 182 A and 185 A Built loop between residues 226 A and 229 A Built loop between residues 182 B and 185 B 2 chains (491 residues) following loop building 2 chains (491 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4434 restraints for refining 4428 atoms. 303 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1892 (Rfree = 0.000) for 4428 atoms. Found 56 (56 requested) and removed 47 (40 requested) atoms. Cycle 17: After refmac, R = 0.1779 (Rfree = 0.000) for 4435 atoms. Found 54 (54 requested) and removed 40 (40 requested) atoms. Cycle 18: After refmac, R = 0.1745 (Rfree = 0.000) for 4446 atoms. Found 53 (53 requested) and removed 42 (40 requested) atoms. Cycle 19: After refmac, R = 0.1718 (Rfree = 0.000) for 4452 atoms. Found 51 (51 requested) and removed 42 (40 requested) atoms. Cycle 20: After refmac, R = 0.1690 (Rfree = 0.000) for 4459 atoms. Found 50 (50 requested) and removed 41 (40 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added, 4469 seeds are put forward Round 1: 488 peptides, 6 chains. Longest chain 171 peptides. Score 0.840 Round 2: 490 peptides, 4 chains. Longest chain 244 peptides. Score 0.848 Round 3: 485 peptides, 9 chains. Longest chain 140 peptides. Score 0.826 Round 4: 481 peptides, 13 chains. Longest chain 108 peptides. Score 0.808 Round 5: 479 peptides, 12 chains. Longest chain 134 peptides. Score 0.810 Taking the results from Round 2 Chains 4, Residues 486, Estimated correctness of the model 95.4 % 4 chains (486 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 246 A and 249 A 2 chains (490 residues) following loop building 2 chains (490 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4518 restraints for refining 4451 atoms. 394 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1896 (Rfree = 0.000) for 4451 atoms. Found 48 (48 requested) and removed 49 (40 requested) atoms. Cycle 22: After refmac, R = 0.1759 (Rfree = 0.000) for 4443 atoms. Found 46 (46 requested) and removed 41 (40 requested) atoms. Cycle 23: After refmac, R = 0.1729 (Rfree = 0.000) for 4444 atoms. Found 45 (45 requested) and removed 42 (40 requested) atoms. Cycle 24: After refmac, R = 0.1697 (Rfree = 0.000) for 4444 atoms. Found 43 (43 requested) and removed 40 (40 requested) atoms. Cycle 25: After refmac, R = 0.1678 (Rfree = 0.000) for 4444 atoms. Found 42 (42 requested) and removed 43 (40 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added (3 deleted due to clashes), 4443 seeds are put forward Round 1: 489 peptides, 5 chains. Longest chain 172 peptides. Score 0.844 Round 2: 489 peptides, 5 chains. Longest chain 223 peptides. Score 0.844 Round 3: 488 peptides, 8 chains. Longest chain 166 peptides. Score 0.832 Round 4: 481 peptides, 12 chains. Longest chain 116 peptides. Score 0.812 Round 5: 476 peptides, 10 chains. Longest chain 130 peptides. Score 0.816 Taking the results from Round 2 Chains 5, Residues 484, Estimated correctness of the model 95.2 % 5 chains (484 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 160 A and 164 A Built loop between residues 220 A and 223 A Built loop between residues 233 B and 236 B 2 chains (491 residues) following loop building 2 chains (491 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4534 restraints for refining 4453 atoms. 401 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1936 (Rfree = 0.000) for 4453 atoms. Found 40 (40 requested) and removed 52 (40 requested) atoms. Cycle 27: After refmac, R = 0.1771 (Rfree = 0.000) for 4438 atoms. Found 40 (40 requested) and removed 43 (40 requested) atoms. Cycle 28: After refmac, R = 0.1734 (Rfree = 0.000) for 4431 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 29: After refmac, R = 0.1700 (Rfree = 0.000) for 4428 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 30: After refmac, R = 0.1682 (Rfree = 0.000) for 4427 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.58 1.91 NCS extension: 0 residues added, 4426 seeds are put forward Round 1: 489 peptides, 5 chains. Longest chain 172 peptides. Score 0.844 Round 2: 489 peptides, 4 chains. Longest chain 166 peptides. Score 0.848 Round 3: 485 peptides, 10 chains. Longest chain 149 peptides. Score 0.822 Round 4: 486 peptides, 6 chains. Longest chain 244 peptides. Score 0.838 Round 5: 468 peptides, 17 chains. Longest chain 97 peptides. Score 0.781 Taking the results from Round 2 Chains 4, Residues 485, Estimated correctness of the model 95.4 % 4 chains (485 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 177 B and 180 B 2 chains (489 residues) following loop building 2 chains (489 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4577 restraints for refining 4454 atoms. 464 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1927 (Rfree = 0.000) for 4454 atoms. Found 40 (40 requested) and removed 53 (40 requested) atoms. Cycle 32: After refmac, R = 0.1749 (Rfree = 0.000) for 4435 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 33: After refmac, R = 0.1713 (Rfree = 0.000) for 4428 atoms. Found 40 (40 requested) and removed 45 (40 requested) atoms. Cycle 34: After refmac, R = 0.1698 (Rfree = 0.000) for 4419 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 35: After refmac, R = 0.1679 (Rfree = 0.000) for 4416 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.60 1.93 NCS extension: 0 residues added, 4416 seeds are put forward Round 1: 487 peptides, 6 chains. Longest chain 172 peptides. Score 0.839 Round 2: 486 peptides, 6 chains. Longest chain 149 peptides. Score 0.838 Round 3: 489 peptides, 5 chains. Longest chain 235 peptides. Score 0.844 Round 4: 484 peptides, 7 chains. Longest chain 149 peptides. Score 0.833 Round 5: 479 peptides, 12 chains. Longest chain 170 peptides. Score 0.810 Taking the results from Round 3 Chains 5, Residues 484, Estimated correctness of the model 95.2 % 4 chains (475 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 177 B and 180 B Built loop between residues 194 B and 197 B 3 chains (488 residues) following loop building 2 chains (479 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4633 restraints for refining 4449 atoms. 574 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1931 (Rfree = 0.000) for 4449 atoms. Found 40 (40 requested) and removed 54 (40 requested) atoms. Cycle 37: After refmac, R = 0.1796 (Rfree = 0.000) for 4430 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 38: After refmac, R = 0.1742 (Rfree = 0.000) for 4423 atoms. Found 40 (40 requested) and removed 43 (40 requested) atoms. Cycle 39: After refmac, R = 0.1715 (Rfree = 0.000) for 4417 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 40: After refmac, R = 0.1712 (Rfree = 0.000) for 4411 atoms. Found 40 (40 requested) and removed 43 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added (10 deleted due to clashes), 4408 seeds are put forward Round 1: 487 peptides, 6 chains. Longest chain 172 peptides. Score 0.839 Round 2: 490 peptides, 5 chains. Longest chain 166 peptides. Score 0.844 Round 3: 486 peptides, 6 chains. Longest chain 213 peptides. Score 0.838 Round 4: 477 peptides, 8 chains. Longest chain 105 peptides. Score 0.825 Round 5: 470 peptides, 16 chains. Longest chain 117 peptides. Score 0.787 Taking the results from Round 2 Chains 5, Residues 485, Estimated correctness of the model 95.2 % 5 chains (485 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 177 A and 180 A Built loop between residues 220 A and 223 A Built loop between residues 143 B and 146 B 2 chains (491 residues) following loop building 2 chains (491 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4503 restraints for refining 4445 atoms. 372 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1929 (Rfree = 0.000) for 4445 atoms. Found 40 (40 requested) and removed 54 (40 requested) atoms. Cycle 42: After refmac, R = 0.1785 (Rfree = 0.000) for 4425 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. Cycle 43: After refmac, R = 0.1749 (Rfree = 0.000) for 4421 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 44: After refmac, R = 0.1725 (Rfree = 0.000) for 4416 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 45: After refmac, R = 0.1709 (Rfree = 0.000) for 4409 atoms. Found 39 (39 requested) and removed 40 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.60 1.93 NCS extension: 0 residues added, 4410 seeds are put forward Round 1: 488 peptides, 5 chains. Longest chain 172 peptides. Score 0.843 Round 2: 490 peptides, 5 chains. Longest chain 209 peptides. Score 0.844 Round 3: 487 peptides, 6 chains. Longest chain 167 peptides. Score 0.839 Round 4: 482 peptides, 10 chains. Longest chain 166 peptides. Score 0.820 Round 5: 471 peptides, 15 chains. Longest chain 80 peptides. Score 0.792 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 485, Estimated correctness of the model 95.2 % 4 chains (476 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 220 B and 223 B 3 chains (489 residues) following loop building 2 chains (480 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 35104 reflections ( 99.87 % complete ) and 4068 restraints for refining 3981 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2554 (Rfree = 0.000) for 3981 atoms. Found 36 (36 requested) and removed 0 (36 requested) atoms. Cycle 47: After refmac, R = 0.2358 (Rfree = 0.000) for 3981 atoms. Found 36 (36 requested) and removed 5 (36 requested) atoms. Cycle 48: After refmac, R = 0.2240 (Rfree = 0.000) for 3981 atoms. Found 36 (36 requested) and removed 13 (36 requested) atoms. Cycle 49: After refmac, R = 0.2174 (Rfree = 0.000) for 3981 atoms. Found 31 (36 requested) and removed 11 (36 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:28:37 GMT 2018 Job finished. TimeTaking 87.67 Used memory is bytes: 22375952