Mon 24 Dec 07:32:09 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 1vlm-2.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-2.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-2.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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/1vlm-2.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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 07:32:13 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/1vlm-2.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.5284 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-2.2-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-2.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.45 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 1 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: 93.922 2.200 Wilson plot Bfac: 29.78 22604 reflections ( 98.93 % complete ) and 0 restraints for refining 3886 atoms. Observations/parameters ratio is 1.45 ------------------------------------------------------ Starting model: R = 0.3366 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2847 (Rfree = 0.000) for 3886 atoms. Found 75 (101 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.26 2.38 NCS extension: 0 residues added, 3909 seeds are put forward Round 1: 238 peptides, 33 chains. Longest chain 22 peptides. Score 0.560 Round 2: 275 peptides, 26 chains. Longest chain 29 peptides. Score 0.728 Round 3: 289 peptides, 22 chains. Longest chain 48 peptides. Score 0.788 Round 4: 307 peptides, 18 chains. Longest chain 66 peptides. Score 0.841 Round 5: 305 peptides, 15 chains. Longest chain 73 peptides. Score 0.858 Taking the results from Round 5 Chains 17, Residues 290, Estimated correctness of the model 97.3 % 7 chains (210 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 B and 93 B Built loop between residues 107 B and 113 B Built loop between residues 197 B and 200 B 14 chains (299 residues) following loop building 4 chains (219 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 4639 restraints for refining 3348 atoms. 2541 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3250 (Rfree = 0.000) for 3348 atoms. Found 87 (87 requested) and removed 51 (43 requested) atoms. Cycle 2: After refmac, R = 0.3006 (Rfree = 0.000) for 3349 atoms. Found 54 (86 requested) and removed 44 (44 requested) atoms. Cycle 3: After refmac, R = 0.2861 (Rfree = 0.000) for 3341 atoms. Found 37 (84 requested) and removed 43 (43 requested) atoms. Cycle 4: After refmac, R = 0.2763 (Rfree = 0.000) for 3319 atoms. Found 48 (82 requested) and removed 21 (43 requested) atoms. Cycle 5: After refmac, R = 0.2658 (Rfree = 0.000) for 3338 atoms. Found 39 (82 requested) and removed 14 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.28 2.41 NCS extension: 186 residues added (62 deleted due to clashes), 3556 seeds are put forward Round 1: 331 peptides, 19 chains. Longest chain 67 peptides. Score 0.862 Round 2: 336 peptides, 11 chains. Longest chain 128 peptides. Score 0.907 Round 3: 339 peptides, 15 chains. Longest chain 59 peptides. Score 0.890 Round 4: 338 peptides, 12 chains. Longest chain 59 peptides. Score 0.904 Round 5: 346 peptides, 12 chains. Longest chain 70 peptides. Score 0.910 Taking the results from Round 5 Chains 12, Residues 334, Estimated correctness of the model 98.8 % 7 chains (295 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 132 A Built loop between residues 90 B and 93 B 10 chains (339 residues) following loop building 5 chains (300 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 4051 restraints for refining 3431 atoms. 1464 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2894 (Rfree = 0.000) for 3431 atoms. Found 69 (84 requested) and removed 62 (44 requested) atoms. Cycle 7: After refmac, R = 0.2663 (Rfree = 0.000) for 3430 atoms. Found 32 (82 requested) and removed 44 (44 requested) atoms. Cycle 8: After refmac, R = 0.2527 (Rfree = 0.000) for 3415 atoms. Found 26 (80 requested) and removed 38 (44 requested) atoms. Cycle 9: After refmac, R = 0.2439 (Rfree = 0.000) for 3400 atoms. Found 22 (77 requested) and removed 20 (44 requested) atoms. Cycle 10: After refmac, R = 0.2378 (Rfree = 0.000) for 3398 atoms. Found 19 (76 requested) and removed 11 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.27 2.39 NCS extension: 64 residues added (127 deleted due to clashes), 3471 seeds are put forward Round 1: 352 peptides, 14 chains. Longest chain 112 peptides. Score 0.905 Round 2: 367 peptides, 9 chains. Longest chain 141 peptides. Score 0.934 Round 3: 364 peptides, 14 chains. Longest chain 76 peptides. Score 0.913 Round 4: 368 peptides, 8 chains. Longest chain 136 peptides. Score 0.939 Round 5: 366 peptides, 15 chains. Longest chain 70 peptides. Score 0.910 Taking the results from Round 4 Chains 9, Residues 360, Estimated correctness of the model 99.4 % 5 chains (345 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 152 B and 159 B 8 chains (366 residues) following loop building 4 chains (351 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3700 restraints for refining 3506 atoms. 751 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2683 (Rfree = 0.000) for 3506 atoms. Found 49 (76 requested) and removed 54 (45 requested) atoms. Cycle 12: After refmac, R = 0.2510 (Rfree = 0.000) for 3499 atoms. Found 42 (75 requested) and removed 45 (45 requested) atoms. Cycle 13: After refmac, R = 0.2395 (Rfree = 0.000) for 3493 atoms. Found 35 (73 requested) and removed 45 (45 requested) atoms. Cycle 14: After refmac, R = 0.2333 (Rfree = 0.000) for 3479 atoms. Found 36 (70 requested) and removed 41 (45 requested) atoms. Cycle 15: After refmac, R = 0.2276 (Rfree = 0.000) for 3472 atoms. Found 35 (68 requested) and removed 41 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.28 2.41 NCS extension: 114 residues added (339 deleted due to clashes), 3584 seeds are put forward Round 1: 368 peptides, 13 chains. Longest chain 97 peptides. Score 0.920 Round 2: 375 peptides, 8 chains. Longest chain 140 peptides. Score 0.942 Round 3: 369 peptides, 12 chains. Longest chain 79 peptides. Score 0.924 Round 4: 365 peptides, 10 chains. Longest chain 124 peptides. Score 0.930 Round 5: 368 peptides, 9 chains. Longest chain 140 peptides. Score 0.935 Taking the results from Round 2 Chains 9, Residues 367, Estimated correctness of the model 99.5 % 6 chains (350 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 198 A Built loop between residues 151 B and 159 B 7 chains (376 residues) following loop building 4 chains (359 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3615 restraints for refining 3497 atoms. 584 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2557 (Rfree = 0.000) for 3497 atoms. Found 67 (67 requested) and removed 55 (45 requested) atoms. Cycle 17: After refmac, R = 0.2393 (Rfree = 0.000) for 3504 atoms. Found 62 (66 requested) and removed 45 (45 requested) atoms. Cycle 18: After refmac, R = 0.2288 (Rfree = 0.000) for 3514 atoms. Found 44 (64 requested) and removed 45 (45 requested) atoms. Cycle 19: After refmac, R = 0.2228 (Rfree = 0.000) for 3511 atoms. Found 52 (62 requested) and removed 29 (45 requested) atoms. Cycle 20: After refmac, R = 0.2162 (Rfree = 0.000) for 3533 atoms. Found 39 (61 requested) and removed 22 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.28 2.41 NCS extension: 101 residues added (360 deleted due to clashes), 3653 seeds are put forward Round 1: 372 peptides, 12 chains. Longest chain 130 peptides. Score 0.926 Round 2: 378 peptides, 9 chains. Longest chain 141 peptides. Score 0.940 Round 3: 384 peptides, 9 chains. Longest chain 124 peptides. Score 0.943 Round 4: 372 peptides, 13 chains. Longest chain 64 peptides. Score 0.922 Round 5: 376 peptides, 13 chains. Longest chain 130 peptides. Score 0.924 Taking the results from Round 3 Chains 9, Residues 375, Estimated correctness of the model 99.5 % 5 chains (354 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 164 A 7 chains (382 residues) following loop building 4 chains (364 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3814 restraints for refining 3574 atoms. 755 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2545 (Rfree = 0.000) for 3574 atoms. Found 60 (60 requested) and removed 54 (46 requested) atoms. Cycle 22: After refmac, R = 0.2393 (Rfree = 0.000) for 3575 atoms. Found 51 (58 requested) and removed 46 (46 requested) atoms. Cycle 23: After refmac, R = 0.2267 (Rfree = 0.000) for 3576 atoms. Found 37 (56 requested) and removed 46 (46 requested) atoms. Cycle 24: After refmac, R = 0.2211 (Rfree = 0.000) for 3559 atoms. Found 44 (54 requested) and removed 35 (46 requested) atoms. Cycle 25: After refmac, R = 0.2178 (Rfree = 0.000) for 3565 atoms. Found 41 (52 requested) and removed 31 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.28 2.41 NCS extension: 35 residues added (139 deleted due to clashes), 3614 seeds are put forward Round 1: 385 peptides, 9 chains. Longest chain 124 peptides. Score 0.943 Round 2: 387 peptides, 9 chains. Longest chain 141 peptides. Score 0.944 Round 3: 389 peptides, 10 chains. Longest chain 130 peptides. Score 0.941 Round 4: 386 peptides, 11 chains. Longest chain 167 peptides. Score 0.937 Round 5: 390 peptides, 10 chains. Longest chain 124 peptides. Score 0.942 Taking the results from Round 2 Chains 11, Residues 378, Estimated correctness of the model 99.5 % 7 chains (366 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 153 A and 164 A Built loop between residues 195 A and 198 A Built loop between residues 151 B and 154 B 5 chains (389 residues) following loop building 3 chains (382 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3566 restraints for refining 3588 atoms. 369 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2500 (Rfree = 0.000) for 3588 atoms. Found 50 (50 requested) and removed 52 (46 requested) atoms. Cycle 27: After refmac, R = 0.2324 (Rfree = 0.000) for 3580 atoms. Found 48 (48 requested) and removed 46 (46 requested) atoms. Cycle 28: After refmac, R = 0.2233 (Rfree = 0.000) for 3579 atoms. Found 40 (46 requested) and removed 46 (46 requested) atoms. Cycle 29: After refmac, R = 0.2185 (Rfree = 0.000) for 3569 atoms. Found 40 (46 requested) and removed 46 (46 requested) atoms. Cycle 30: After refmac, R = 0.2155 (Rfree = 0.000) for 3562 atoms. Found 46 (46 requested) and removed 27 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.27 2.39 NCS extension: 46 residues added (192 deleted due to clashes), 3630 seeds are put forward Round 1: 388 peptides, 11 chains. Longest chain 98 peptides. Score 0.938 Round 2: 394 peptides, 7 chains. Longest chain 141 peptides. Score 0.953 Round 3: 392 peptides, 9 chains. Longest chain 130 peptides. Score 0.946 Round 4: 392 peptides, 12 chains. Longest chain 136 peptides. Score 0.936 Round 5: 381 peptides, 13 chains. Longest chain 141 peptides. Score 0.927 Taking the results from Round 2 Chains 7, Residues 387, Estimated correctness of the model 99.6 % 5 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 198 A Built loop between residues 152 B and 158 B 5 chains (394 residues) following loop building 3 chains (388 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3546 restraints for refining 3595 atoms. 312 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2395 (Rfree = 0.000) for 3595 atoms. Found 46 (46 requested) and removed 51 (46 requested) atoms. Cycle 32: After refmac, R = 0.2262 (Rfree = 0.000) for 3585 atoms. Found 46 (46 requested) and removed 46 (46 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2186 (Rfree = 0.000) for 3584 atoms. Found 41 (46 requested) and removed 46 (46 requested) atoms. Cycle 34: After refmac, R = 0.2126 (Rfree = 0.000) for 3577 atoms. Found 43 (46 requested) and removed 46 (46 requested) atoms. Cycle 35: After refmac, R = 0.2107 (Rfree = 0.000) for 3574 atoms. Found 43 (46 requested) and removed 43 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.27 2.39 NCS extension: 34 residues added (195 deleted due to clashes), 3611 seeds are put forward Round 1: 389 peptides, 8 chains. Longest chain 98 peptides. Score 0.948 Round 2: 386 peptides, 9 chains. Longest chain 130 peptides. Score 0.943 Round 3: 387 peptides, 9 chains. Longest chain 79 peptides. Score 0.944 Round 4: 384 peptides, 13 chains. Longest chain 118 peptides. Score 0.929 Round 5: 391 peptides, 6 chains. Longest chain 141 peptides. Score 0.955 Taking the results from Round 5 Chains 6, Residues 385, Estimated correctness of the model 99.7 % 4 chains (379 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 152 B and 159 B 5 chains (391 residues) following loop building 3 chains (385 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3594 restraints for refining 3591 atoms. 383 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2403 (Rfree = 0.000) for 3591 atoms. Found 46 (46 requested) and removed 48 (46 requested) atoms. Cycle 37: After refmac, R = 0.2237 (Rfree = 0.000) for 3583 atoms. Found 46 (46 requested) and removed 46 (46 requested) atoms. Cycle 38: After refmac, R = 0.2177 (Rfree = 0.000) for 3582 atoms. Found 39 (46 requested) and removed 46 (46 requested) atoms. Cycle 39: After refmac, R = 0.2128 (Rfree = 0.000) for 3575 atoms. Found 46 (46 requested) and removed 46 (46 requested) atoms. Cycle 40: After refmac, R = 0.2097 (Rfree = 0.000) for 3572 atoms. Found 42 (46 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.27 2.39 NCS extension: 32 residues added (200 deleted due to clashes), 3602 seeds are put forward Round 1: 388 peptides, 6 chains. Longest chain 141 peptides. Score 0.954 Round 2: 393 peptides, 12 chains. Longest chain 79 peptides. Score 0.936 Round 3: 390 peptides, 8 chains. Longest chain 141 peptides. Score 0.948 Round 4: 395 peptides, 10 chains. Longest chain 130 peptides. Score 0.944 Round 5: 397 peptides, 7 chains. Longest chain 137 peptides. Score 0.954 Taking the results from Round 5 Chains 8, Residues 390, Estimated correctness of the model 99.7 % 5 chains (379 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 82 A Built loop between residues 90 B and 93 B 6 chains (400 residues) following loop building 3 chains (389 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3721 restraints for refining 3643 atoms. 464 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2496 (Rfree = 0.000) for 3643 atoms. Found 47 (47 requested) and removed 56 (47 requested) atoms. Cycle 42: After refmac, R = 0.2312 (Rfree = 0.000) for 3628 atoms. Found 47 (47 requested) and removed 48 (47 requested) atoms. Cycle 43: After refmac, R = 0.2209 (Rfree = 0.000) for 3625 atoms. Found 37 (47 requested) and removed 47 (47 requested) atoms. Cycle 44: After refmac, R = 0.2157 (Rfree = 0.000) for 3613 atoms. Found 33 (47 requested) and removed 47 (47 requested) atoms. Cycle 45: After refmac, R = 0.2128 (Rfree = 0.000) for 3597 atoms. Found 37 (46 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.27 2.39 NCS extension: 34 residues added (187 deleted due to clashes), 3623 seeds are put forward Round 1: 395 peptides, 7 chains. Longest chain 141 peptides. Score 0.953 Round 2: 400 peptides, 6 chains. Longest chain 141 peptides. Score 0.958 Round 3: 398 peptides, 10 chains. Longest chain 79 peptides. Score 0.945 Round 4: 400 peptides, 7 chains. Longest chain 135 peptides. Score 0.955 Round 5: 389 peptides, 16 chains. Longest chain 79 peptides. Score 0.920 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 394, Estimated correctness of the model 99.7 % 6 chains (382 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 64 A and 78 A Built loop between residues 195 A and 198 A Built loop between residues 152 B and 158 B Built loop between residues 177 B and 180 B 4 chains (407 residues) following loop building 2 chains (404 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22604 reflections ( 98.93 % complete ) and 3358 restraints for refining 3290 atoms. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2843 (Rfree = 0.000) for 3290 atoms. Found 20 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2632 (Rfree = 0.000) for 3290 atoms. Found 5 (43 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2515 (Rfree = 0.000) for 3290 atoms. Found 7 (43 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2443 (Rfree = 0.000) for 3290 atoms. TimeTaking 47.62