Sun 23 Dec 22:22:50 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 2ajr-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-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/2ajr-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-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 ============================================================ Sun 23 Dec 22:22:59 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/2ajr-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-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 684 and 0 Target number of residues in the AU: 684 Target solvent content: 0.5571 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-2.5-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 5296 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: 29.168 2.457 Wilson plot Bfac: 37.46 31336 reflections ( 99.47 % complete ) and 0 restraints for refining 5886 atoms. Observations/parameters ratio is 1.33 ------------------------------------------------------ Starting model: R = 0.3650 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3112 (Rfree = 0.000) for 5886 atoms. Found 45 (112 requested) and removed 116 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.60 2.37 NCS extension: 0 residues added, 5815 seeds are put forward Round 1: 346 peptides, 66 chains. Longest chain 12 peptides. Score 0.345 Round 2: 365 peptides, 58 chains. Longest chain 24 peptides. Score 0.447 Round 3: 384 peptides, 53 chains. Longest chain 18 peptides. Score 0.519 Round 4: 404 peptides, 55 chains. Longest chain 24 peptides. Score 0.537 Round 5: 411 peptides, 53 chains. Longest chain 32 peptides. Score 0.562 Taking the results from Round 5 Chains 55, Residues 358, Estimated correctness of the model 69.8 % 7 chains (72 residues) have been docked in sequence ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 9875 restraints for refining 4973 atoms. 8239 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3654 (Rfree = 0.000) for 4973 atoms. Found 94 (94 requested) and removed 84 (47 requested) atoms. Cycle 2: After refmac, R = 0.3387 (Rfree = 0.000) for 4954 atoms. Found 81 (94 requested) and removed 60 (47 requested) atoms. Cycle 3: After refmac, R = 0.3256 (Rfree = 0.000) for 4951 atoms. Found 58 (94 requested) and removed 60 (47 requested) atoms. Cycle 4: After refmac, R = 0.3180 (Rfree = 0.000) for 4927 atoms. Found 60 (94 requested) and removed 54 (47 requested) atoms. Cycle 5: After refmac, R = 0.3050 (Rfree = 0.000) for 4918 atoms. Found 43 (94 requested) and removed 51 (47 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.61 2.38 NCS extension: 7 residues added (0 deleted due to clashes), 4945 seeds are put forward Round 1: 410 peptides, 57 chains. Longest chain 38 peptides. Score 0.532 Round 2: 441 peptides, 51 chains. Longest chain 28 peptides. Score 0.619 Round 3: 480 peptides, 53 chains. Longest chain 22 peptides. Score 0.658 Round 4: 468 peptides, 50 chains. Longest chain 43 peptides. Score 0.661 Round 5: 488 peptides, 52 chains. Longest chain 42 peptides. Score 0.674 Taking the results from Round 5 Chains 55, Residues 436, Estimated correctness of the model 82.4 % 7 chains (83 residues) have been docked in sequence ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 9430 restraints for refining 4974 atoms. 7462 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3367 (Rfree = 0.000) for 4974 atoms. Found 94 (94 requested) and removed 76 (47 requested) atoms. Cycle 7: After refmac, R = 0.3316 (Rfree = 0.000) for 4975 atoms. Found 95 (95 requested) and removed 63 (47 requested) atoms. Cycle 8: After refmac, R = 0.3140 (Rfree = 0.000) for 4995 atoms. Found 83 (95 requested) and removed 54 (47 requested) atoms. Cycle 9: After refmac, R = 0.3032 (Rfree = 0.000) for 5013 atoms. Found 85 (95 requested) and removed 55 (47 requested) atoms. Cycle 10: After refmac, R = 0.2805 (Rfree = 0.000) for 5026 atoms. Found 44 (96 requested) and removed 51 (48 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.57 2.34 NCS extension: 10 residues added (1 deleted due to clashes), 5075 seeds are put forward Round 1: 432 peptides, 47 chains. Longest chain 30 peptides. Score 0.632 Round 2: 457 peptides, 39 chains. Longest chain 37 peptides. Score 0.710 Round 3: 478 peptides, 42 chains. Longest chain 32 peptides. Score 0.717 Round 4: 476 peptides, 43 chains. Longest chain 34 peptides. Score 0.709 Round 5: 476 peptides, 45 chains. Longest chain 32 peptides. Score 0.698 Taking the results from Round 3 Chains 44, Residues 436, Estimated correctness of the model 86.4 % 11 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 140 B and 145 B 43 chains (439 residues) following loop building 10 chains (203 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 8104 restraints for refining 4973 atoms. 5610 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3260 (Rfree = 0.000) for 4973 atoms. Found 94 (94 requested) and removed 71 (47 requested) atoms. Cycle 12: After refmac, R = 0.3024 (Rfree = 0.000) for 4982 atoms. Found 84 (93 requested) and removed 54 (47 requested) atoms. Cycle 13: After refmac, R = 0.2929 (Rfree = 0.000) for 4993 atoms. Found 83 (91 requested) and removed 52 (47 requested) atoms. Cycle 14: After refmac, R = 0.2878 (Rfree = 0.000) for 5010 atoms. Found 64 (89 requested) and removed 47 (47 requested) atoms. Cycle 15: After refmac, R = 0.2931 (Rfree = 0.000) for 5008 atoms. Found 77 (87 requested) and removed 51 (47 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.57 2.34 NCS extension: 18 residues added (13 deleted due to clashes), 5077 seeds are put forward Round 1: 449 peptides, 44 chains. Longest chain 29 peptides. Score 0.672 Round 2: 474 peptides, 41 chains. Longest chain 45 peptides. Score 0.718 Round 3: 482 peptides, 42 chains. Longest chain 30 peptides. Score 0.721 Round 4: 495 peptides, 44 chains. Longest chain 31 peptides. Score 0.725 Round 5: 498 peptides, 37 chains. Longest chain 38 peptides. Score 0.762 Taking the results from Round 5 Chains 41, Residues 461, Estimated correctness of the model 90.1 % 10 chains (210 residues) have been docked in sequence Building loops using Loopy2018 41 chains (461 residues) following loop building 10 chains (210 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 7874 restraints for refining 4973 atoms. 5254 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3206 (Rfree = 0.000) for 4973 atoms. Found 85 (85 requested) and removed 60 (47 requested) atoms. Cycle 17: After refmac, R = 0.2947 (Rfree = 0.000) for 4983 atoms. Found 84 (84 requested) and removed 54 (47 requested) atoms. Cycle 18: After refmac, R = 0.2887 (Rfree = 0.000) for 4996 atoms. Found 78 (82 requested) and removed 49 (47 requested) atoms. Cycle 19: After refmac, R = 0.2642 (Rfree = 0.000) for 5011 atoms. Found 39 (80 requested) and removed 49 (47 requested) atoms. Cycle 20: After refmac, R = 0.2583 (Rfree = 0.000) for 4992 atoms. Found 31 (78 requested) and removed 49 (47 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.54 2.31 NCS extension: 35 residues added (16 deleted due to clashes), 5027 seeds are put forward Round 1: 498 peptides, 47 chains. Longest chain 32 peptides. Score 0.712 Round 2: 515 peptides, 37 chains. Longest chain 35 peptides. Score 0.777 Round 3: 503 peptides, 37 chains. Longest chain 54 peptides. Score 0.766 Round 4: 507 peptides, 36 chains. Longest chain 38 peptides. Score 0.774 Round 5: 503 peptides, 38 chains. Longest chain 38 peptides. Score 0.762 Taking the results from Round 2 Chains 40, Residues 478, Estimated correctness of the model 91.2 % 13 chains (292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 71 A Built loop between residues 308 A and 311 A 37 chains (484 residues) following loop building 11 chains (300 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 6942 restraints for refining 4974 atoms. 3916 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2969 (Rfree = 0.000) for 4974 atoms. Found 75 (75 requested) and removed 62 (47 requested) atoms. Cycle 22: After refmac, R = 0.2795 (Rfree = 0.000) for 4972 atoms. Found 67 (74 requested) and removed 53 (47 requested) atoms. Cycle 23: After refmac, R = 0.2713 (Rfree = 0.000) for 4981 atoms. Found 46 (72 requested) and removed 53 (47 requested) atoms. Cycle 24: After refmac, R = 0.2691 (Rfree = 0.000) for 4961 atoms. Found 53 (70 requested) and removed 49 (47 requested) atoms. Cycle 25: After refmac, R = 0.2564 (Rfree = 0.000) for 4953 atoms. Found 42 (68 requested) and removed 49 (47 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.53 2.30 NCS extension: 51 residues added (44 deleted due to clashes), 5021 seeds are put forward Round 1: 493 peptides, 44 chains. Longest chain 38 peptides. Score 0.722 Round 2: 516 peptides, 37 chains. Longest chain 38 peptides. Score 0.778 Round 3: 504 peptides, 34 chains. Longest chain 54 peptides. Score 0.781 Round 4: 512 peptides, 31 chains. Longest chain 58 peptides. Score 0.800 Round 5: 513 peptides, 34 chains. Longest chain 54 peptides. Score 0.788 Taking the results from Round 4 Chains 36, Residues 481, Estimated correctness of the model 92.8 % 15 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 B and 145 B 35 chains (488 residues) following loop building 14 chains (368 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 6887 restraints for refining 5127 atoms. 3480 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2820 (Rfree = 0.000) for 5127 atoms. Found 68 (68 requested) and removed 55 (48 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2714 (Rfree = 0.000) for 5121 atoms. Found 53 (66 requested) and removed 53 (48 requested) atoms. Cycle 28: After refmac, R = 0.2666 (Rfree = 0.000) for 5116 atoms. Found 53 (64 requested) and removed 51 (48 requested) atoms. Cycle 29: After refmac, R = 0.2613 (Rfree = 0.000) for 5113 atoms. Found 49 (62 requested) and removed 52 (48 requested) atoms. Cycle 30: After refmac, R = 0.2613 (Rfree = 0.000) for 5106 atoms. Found 50 (60 requested) and removed 50 (48 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.53 2.30 NCS extension: 44 residues added (39 deleted due to clashes), 5165 seeds are put forward Round 1: 511 peptides, 34 chains. Longest chain 56 peptides. Score 0.787 Round 2: 520 peptides, 28 chains. Longest chain 54 peptides. Score 0.819 Round 3: 520 peptides, 30 chains. Longest chain 72 peptides. Score 0.811 Round 4: 506 peptides, 28 chains. Longest chain 54 peptides. Score 0.808 Round 5: 505 peptides, 30 chains. Longest chain 54 peptides. Score 0.799 Taking the results from Round 2 Chains 31, Residues 492, Estimated correctness of the model 94.0 % 15 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 117 A Built loop between residues 241 A and 244 A Built loop between residues 306 A and 311 A Built loop between residues 42 B and 48 B Built loop between residues 70 B and 81 B 25 chains (516 residues) following loop building 10 chains (407 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 6603 restraints for refining 5166 atoms. 2973 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2690 (Rfree = 0.000) for 5166 atoms. Found 59 (59 requested) and removed 66 (49 requested) atoms. Cycle 32: After refmac, R = 0.2569 (Rfree = 0.000) for 5150 atoms. Found 57 (57 requested) and removed 50 (49 requested) atoms. Cycle 33: After refmac, R = 0.2508 (Rfree = 0.000) for 5152 atoms. Found 52 (55 requested) and removed 50 (49 requested) atoms. Cycle 34: After refmac, R = 0.2406 (Rfree = 0.000) for 5152 atoms. Found 48 (53 requested) and removed 49 (49 requested) atoms. Cycle 35: After refmac, R = 0.2412 (Rfree = 0.000) for 5145 atoms. Found 46 (51 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.53 2.30 NCS extension: 98 residues added (74 deleted due to clashes), 5245 seeds are put forward Round 1: 530 peptides, 26 chains. Longest chain 69 peptides. Score 0.833 Round 2: 536 peptides, 27 chains. Longest chain 73 peptides. Score 0.834 Round 3: 549 peptides, 27 chains. Longest chain 81 peptides. Score 0.842 Round 4: 546 peptides, 29 chains. Longest chain 61 peptides. Score 0.833 Round 5: 537 peptides, 26 chains. Longest chain 96 peptides. Score 0.838 Taking the results from Round 3 Chains 33, Residues 522, Estimated correctness of the model 95.3 % 16 chains (404 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 101 A and 107 A Built loop between residues 213 A and 215 A Built loop between residues 274 A and 278 A Built loop between residues 304 A and 313 A Built loop between residues 43 B and 50 B Built loop between residues 80 B and 83 B Built loop between residues 116 B and 119 B 22 chains (546 residues) following loop building 8 chains (435 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 6300 restraints for refining 5186 atoms. 2425 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2586 (Rfree = 0.000) for 5186 atoms. Found 49 (49 requested) and removed 56 (49 requested) atoms. Cycle 37: After refmac, R = 0.2432 (Rfree = 0.000) for 5163 atoms. Found 49 (49 requested) and removed 51 (49 requested) atoms. Cycle 38: After refmac, R = 0.2342 (Rfree = 0.000) for 5155 atoms. Found 49 (49 requested) and removed 51 (49 requested) atoms. Cycle 39: After refmac, R = 0.2312 (Rfree = 0.000) for 5150 atoms. Found 46 (49 requested) and removed 51 (49 requested) atoms. Cycle 40: After refmac, R = 0.2278 (Rfree = 0.000) for 5136 atoms. Found 49 (49 requested) and removed 53 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.53 2.30 NCS extension: 58 residues added (85 deleted due to clashes), 5205 seeds are put forward Round 1: 553 peptides, 23 chains. Longest chain 68 peptides. Score 0.859 Round 2: 563 peptides, 18 chains. Longest chain 109 peptides. Score 0.880 Round 3: 560 peptides, 27 chains. Longest chain 105 peptides. Score 0.849 Round 4: 567 peptides, 21 chains. Longest chain 91 peptides. Score 0.873 Round 5: 558 peptides, 25 chains. Longest chain 89 peptides. Score 0.855 Taking the results from Round 2 Chains 22, Residues 545, Estimated correctness of the model 97.2 % 12 chains (474 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 38 A Built loop between residues 141 A and 144 A Built loop between residues 210 A and 215 A Built loop between residues 63 B and 67 B Built loop between residues 284 B and 288 B 15 chains (559 residues) following loop building 7 chains (493 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 5963 restraints for refining 5193 atoms. 1783 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2444 (Rfree = 0.000) for 5193 atoms. Found 49 (49 requested) and removed 68 (49 requested) atoms. Cycle 42: After refmac, R = 0.2325 (Rfree = 0.000) for 5161 atoms. Found 49 (49 requested) and removed 50 (49 requested) atoms. Cycle 43: After refmac, R = 0.2246 (Rfree = 0.000) for 5156 atoms. Found 46 (49 requested) and removed 50 (49 requested) atoms. Cycle 44: After refmac, R = 0.2192 (Rfree = 0.000) for 5147 atoms. Found 49 (49 requested) and removed 53 (49 requested) atoms. Cycle 45: After refmac, R = 0.2165 (Rfree = 0.000) for 5138 atoms. Found 48 (49 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.51 2.29 NCS extension: 234 residues added (187 deleted due to clashes), 5376 seeds are put forward Round 1: 565 peptides, 22 chains. Longest chain 68 peptides. Score 0.869 Round 2: 584 peptides, 15 chains. Longest chain 158 peptides. Score 0.899 Round 3: 582 peptides, 20 chains. Longest chain 78 peptides. Score 0.884 Round 4: 578 peptides, 20 chains. Longest chain 125 peptides. Score 0.882 Round 5: 575 peptides, 20 chains. Longest chain 120 peptides. Score 0.880 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 569, Estimated correctness of the model 97.9 % 12 chains (512 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 90 A and 97 A Built loop between residues 129 A and 133 A Built loop between residues 268 A and 271 A Built loop between residues 283 A and 290 A Built loop between residues 169 B and 177 B Built loop between residues 309 B and 312 B 17 chains (592 residues) following loop building 6 chains (538 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 31336 reflections ( 99.47 % complete ) and 4546 restraints for refining 4481 atoms. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3010 (Rfree = 0.000) for 4481 atoms. Found 42 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2820 (Rfree = 0.000) for 4481 atoms. Found 22 (43 requested) and removed 2 (43 requested) atoms. Cycle 48: After refmac, R = 0.2736 (Rfree = 0.000) for 4481 atoms. Found 18 (43 requested) and removed 5 (43 requested) atoms. Cycle 49: After refmac, R = 0.2682 (Rfree = 0.000) for 4481 atoms. TimeTaking 84.15