Sun 23 Dec 22:23:02 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 2a6b-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-2.1-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/2a6b-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-2.1-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 22:23:12 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/2a6b-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-2.1-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 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.4025 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.23 Input MTZ file: 2a6b-2.1-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: 90 Cell parameters: 119.176 119.176 46.302 90.000 90.000 90.000 Input sequence file: 2a6b-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.25 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: 29.794 2.100 Wilson plot Bfac: 8.26 20012 reflections ( 99.81 % complete ) and 0 restraints for refining 7576 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3252 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2806 (Rfree = 0.000) for 7576 atoms. Found 43 (225 requested) and removed 603 (112 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.72 2.57 NCS extension: 0 residues added, 7016 seeds are put forward Round 1: 170 peptides, 18 chains. Longest chain 23 peptides. Score 0.640 Round 2: 191 peptides, 13 chains. Longest chain 68 peptides. Score 0.768 Round 3: 194 peptides, 9 chains. Longest chain 71 peptides. Score 0.819 Round 4: 204 peptides, 6 chains. Longest chain 80 peptides. Score 0.865 Round 5: 202 peptides, 9 chains. Longest chain 51 peptides. Score 0.834 Taking the results from Round 4 Chains 6, Residues 198, Estimated correctness of the model 97.9 % 5 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 B and 45 B Built loop between residues 123 B and 126 B Built loop between residues 204 B and 210 B 3 chains (207 residues) following loop building 2 chains (197 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 4488 restraints for refining 3592 atoms. 2818 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3342 (Rfree = 0.000) for 3592 atoms. Found 99 (107 requested) and removed 117 (53 requested) atoms. Cycle 2: After refmac, R = 0.3046 (Rfree = 0.000) for 3526 atoms. Found 80 (104 requested) and removed 85 (53 requested) atoms. Cycle 3: After refmac, R = 0.2826 (Rfree = 0.000) for 3489 atoms. Found 84 (100 requested) and removed 69 (52 requested) atoms. Cycle 4: After refmac, R = 0.2733 (Rfree = 0.000) for 3478 atoms. Found 71 (98 requested) and removed 60 (52 requested) atoms. Cycle 5: After refmac, R = 0.2673 (Rfree = 0.000) for 3477 atoms. Found 86 (95 requested) and removed 55 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 2.45 NCS extension: 136 residues added (15 deleted due to clashes), 3646 seeds are put forward Round 1: 206 peptides, 5 chains. Longest chain 124 peptides. Score 0.876 Round 2: 209 peptides, 4 chains. Longest chain 101 peptides. Score 0.888 Round 3: 206 peptides, 4 chains. Longest chain 125 peptides. Score 0.884 Round 4: 210 peptides, 5 chains. Longest chain 111 peptides. Score 0.881 Round 5: 212 peptides, 5 chains. Longest chain 91 peptides. Score 0.884 Taking the results from Round 2 Chains 5, Residues 205, Estimated correctness of the model 98.5 % 4 chains (204 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A Built loop between residues 169 A and 173 A Built loop between residues 205 A and 210 A 1 chains (213 residues) following loop building 1 chains (213 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3821 restraints for refining 3337 atoms. 2043 conditional restraints added. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2988 (Rfree = 0.000) for 3337 atoms. Found 89 (89 requested) and removed 58 (49 requested) atoms. Cycle 7: After refmac, R = 0.2775 (Rfree = 0.000) for 3351 atoms. Found 76 (88 requested) and removed 51 (50 requested) atoms. Cycle 8: After refmac, R = 0.2576 (Rfree = 0.000) for 3367 atoms. Found 73 (86 requested) and removed 50 (50 requested) atoms. Cycle 9: After refmac, R = 0.2542 (Rfree = 0.000) for 3369 atoms. Found 55 (84 requested) and removed 51 (50 requested) atoms. Cycle 10: After refmac, R = 0.2418 (Rfree = 0.000) for 3363 atoms. Found 57 (82 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.60 2.39 NCS extension: 0 residues added, 3370 seeds are put forward Round 1: 209 peptides, 3 chains. Longest chain 151 peptides. Score 0.896 Round 2: 210 peptides, 5 chains. Longest chain 99 peptides. Score 0.881 Round 3: 212 peptides, 3 chains. Longest chain 153 peptides. Score 0.900 Round 4: 213 peptides, 3 chains. Longest chain 152 peptides. Score 0.901 Round 5: 212 peptides, 3 chains. Longest chain 103 peptides. Score 0.900 Taking the results from Round 4 Chains 3, Residues 210, Estimated correctness of the model 98.8 % 3 chains (210 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 204 A and 210 A 2 chains (215 residues) following loop building 2 chains (215 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3521 restraints for refining 3238 atoms. 1717 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2857 (Rfree = 0.000) for 3238 atoms. Found 77 (77 requested) and removed 55 (48 requested) atoms. Cycle 12: After refmac, R = 0.2557 (Rfree = 0.000) for 3247 atoms. Found 74 (76 requested) and removed 48 (48 requested) atoms. Cycle 13: After refmac, R = 0.2441 (Rfree = 0.000) for 3263 atoms. Found 61 (74 requested) and removed 50 (48 requested) atoms. Cycle 14: After refmac, R = 0.2341 (Rfree = 0.000) for 3261 atoms. Found 70 (72 requested) and removed 48 (48 requested) atoms. Cycle 15: After refmac, R = 0.2317 (Rfree = 0.000) for 3275 atoms. Found 59 (70 requested) and removed 48 (48 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.63 2.44 NCS extension: 184 residues added (9 deleted due to clashes), 3471 seeds are put forward Round 1: 209 peptides, 3 chains. Longest chain 152 peptides. Score 0.896 Round 2: 212 peptides, 4 chains. Longest chain 147 peptides. Score 0.892 Round 3: 212 peptides, 3 chains. Longest chain 135 peptides. Score 0.900 Round 4: 211 peptides, 3 chains. Longest chain 118 peptides. Score 0.898 Round 5: 207 peptides, 7 chains. Longest chain 97 peptides. Score 0.860 Taking the results from Round 3 Chains 4, Residues 209, Estimated correctness of the model 98.8 % 3 chains (205 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 73 A Built loop between residues 202 A and 210 A 1 chains (217 residues) following loop building 1 chains (217 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3384 restraints for refining 3176 atoms. 1563 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2747 (Rfree = 0.000) for 3176 atoms. Found 66 (66 requested) and removed 52 (47 requested) atoms. Cycle 17: After refmac, R = 0.2434 (Rfree = 0.000) for 3184 atoms. Found 65 (65 requested) and removed 48 (47 requested) atoms. Cycle 18: After refmac, R = 0.2307 (Rfree = 0.000) for 3189 atoms. Found 63 (63 requested) and removed 47 (47 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2252 (Rfree = 0.000) for 3196 atoms. Found 61 (61 requested) and removed 44 (47 requested) atoms. Cycle 20: After refmac, R = 0.2218 (Rfree = 0.000) for 3203 atoms. Found 59 (59 requested) and removed 34 (47 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.63 2.44 NCS extension: 249 residues added (14 deleted due to clashes), 3478 seeds are put forward Round 1: 213 peptides, 2 chains. Longest chain 188 peptides. Score 0.908 Round 2: 208 peptides, 4 chains. Longest chain 114 peptides. Score 0.887 Round 3: 212 peptides, 4 chains. Longest chain 112 peptides. Score 0.892 Round 4: 212 peptides, 3 chains. Longest chain 121 peptides. Score 0.900 Round 5: 211 peptides, 4 chains. Longest chain 135 peptides. Score 0.891 Taking the results from Round 1 Chains 2, Residues 211, Estimated correctness of the model 98.9 % 2 chains (211 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 204 A and 209 A 1 chains (215 residues) following loop building 1 chains (215 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3449 restraints for refining 3168 atoms. 1645 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2617 (Rfree = 0.000) for 3168 atoms. Found 56 (56 requested) and removed 53 (47 requested) atoms. Cycle 22: After refmac, R = 0.2381 (Rfree = 0.000) for 3168 atoms. Found 55 (55 requested) and removed 37 (47 requested) atoms. Cycle 23: After refmac, R = 0.2298 (Rfree = 0.000) for 3182 atoms. Found 53 (53 requested) and removed 28 (47 requested) atoms. Cycle 24: After refmac, R = 0.2217 (Rfree = 0.000) for 3201 atoms. Found 51 (51 requested) and removed 36 (47 requested) atoms. Cycle 25: After refmac, R = 0.2180 (Rfree = 0.000) for 3212 atoms. Found 49 (49 requested) and removed 28 (47 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.61 2.41 NCS extension: 0 residues added, 3233 seeds are put forward Round 1: 210 peptides, 3 chains. Longest chain 153 peptides. Score 0.897 Round 2: 211 peptides, 3 chains. Longest chain 157 peptides. Score 0.898 Round 3: 208 peptides, 6 chains. Longest chain 80 peptides. Score 0.870 Round 4: 208 peptides, 7 chains. Longest chain 67 peptides. Score 0.862 Round 5: 205 peptides, 4 chains. Longest chain 85 peptides. Score 0.883 Taking the results from Round 2 Chains 3, Residues 208, Estimated correctness of the model 98.7 % 3 chains (208 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 205 A and 211 A 1 chains (215 residues) following loop building 1 chains (215 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3495 restraints for refining 3179 atoms. 1691 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2627 (Rfree = 0.000) for 3179 atoms. Found 47 (47 requested) and removed 54 (47 requested) atoms. Cycle 27: After refmac, R = 0.2396 (Rfree = 0.000) for 3170 atoms. Found 47 (47 requested) and removed 25 (47 requested) atoms. Cycle 28: After refmac, R = 0.2324 (Rfree = 0.000) for 3182 atoms. Found 47 (47 requested) and removed 25 (47 requested) atoms. Cycle 29: After refmac, R = 0.2232 (Rfree = 0.000) for 3199 atoms. Found 47 (47 requested) and removed 21 (47 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 3215 atoms. Found 48 (48 requested) and removed 24 (48 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.63 2.44 NCS extension: 0 residues added, 3240 seeds are put forward Round 1: 207 peptides, 4 chains. Longest chain 119 peptides. Score 0.886 Round 2: 207 peptides, 6 chains. Longest chain 98 peptides. Score 0.869 Round 3: 209 peptides, 5 chains. Longest chain 87 peptides. Score 0.880 Round 4: 205 peptides, 8 chains. Longest chain 65 peptides. Score 0.848 Round 5: 208 peptides, 5 chains. Longest chain 85 peptides. Score 0.879 Taking the results from Round 1 Chains 4, Residues 203, Estimated correctness of the model 98.4 % 4 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 167 A and 172 A Built loop between residues 204 A and 211 A 1 chains (215 residues) following loop building 1 chains (215 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3587 restraints for refining 3208 atoms. 1783 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2527 (Rfree = 0.000) for 3208 atoms. Found 47 (47 requested) and removed 53 (47 requested) atoms. Cycle 32: After refmac, R = 0.2391 (Rfree = 0.000) for 3194 atoms. Found 47 (47 requested) and removed 32 (47 requested) atoms. Cycle 33: After refmac, R = 0.2326 (Rfree = 0.000) for 3208 atoms. Found 47 (47 requested) and removed 17 (47 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 3232 atoms. Found 48 (48 requested) and removed 16 (48 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 3254 atoms. Found 48 (48 requested) and removed 31 (48 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.62 2.42 NCS extension: 0 residues added, 3273 seeds are put forward Round 1: 207 peptides, 4 chains. Longest chain 99 peptides. Score 0.886 Round 2: 207 peptides, 5 chains. Longest chain 112 peptides. Score 0.877 Round 3: 206 peptides, 5 chains. Longest chain 67 peptides. Score 0.876 Round 4: 204 peptides, 8 chains. Longest chain 61 peptides. Score 0.847 Round 5: 208 peptides, 5 chains. Longest chain 100 peptides. Score 0.879 Taking the results from Round 1 Chains 4, Residues 203, Estimated correctness of the model 98.4 % 4 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A Built loop between residues 168 A and 172 A Built loop between residues 204 A and 211 A 1 chains (214 residues) following loop building 1 chains (214 residues) in sequence following loop building ------------------------------------------------------ 20012 reflections ( 99.81 % complete ) and 3643 restraints for refining 3231 atoms. 1852 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2586 (Rfree = 0.000) for 3231 atoms. Found 48 (48 requested) and removed 55 (48 requested) atoms. Cycle 37: After refmac, R = 0.2422 (Rfree = 0.000) for 3220 atoms. Found 48 (48 requested) and removed 29 (48 requested) atoms. Cycle 38: After refmac, R = 0.2359 (Rfree = 0.000) for 3234 atoms. Found 48 (48 requested) and removed 14 (48 requested) atoms. Cycle 39: After refmac, R = 0.2307 (Rfree = 0.000) for 3267 atoms. Found 47 (48 requested) and removed 26 (48 requested) atoms. Cycle 40: After refmac, R = 0.2292 (Rfree = 0.000) for 3283 atoms. Found 48 (48 requested) and removed 25 (48 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.61 2.41 NCS extension: 0 residues added, 3307 seeds are put forward Round 1: 207 peptides, 4 chains. Longest chain 112 peptides. Score 0.886 Round 2: 207 peptides, 5 chains. Longest chain 98 peptides. Score 0.877 Round 3: 209 peptides, 3 chains. Longest chain 151 peptides. Score 0.896 Round 4: 207 peptides, 8 chains. Longest chain 47 peptides. Score 0.851 Round 5: 208 peptides, 6 chains. Longest chain 89 peptides. Score 0.870 Taking the results from Round 3 Chains 3, Residues 206, Estimated correctness of the model 98.7 % 3 chains (206 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 172 A Built loop between residues 204 A and 210 A 1 chains (215 residues) following loop building 1 chains (215 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 20012 reflections ( 99.81 % complete ) and 3604 restraints for refining 3244 atoms. 1800 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2507 (Rfree = 0.000) for 3244 atoms. Found 48 (48 requested) and removed 51 (48 requested) atoms. Cycle 42: After refmac, R = 0.2278 (Rfree = 0.000) for 3230 atoms. Found 48 (48 requested) and removed 26 (48 requested) atoms. Cycle 43: After refmac, R = 0.2217 (Rfree = 0.000) for 3245 atoms. Found 48 (48 requested) and removed 26 (48 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 3255 atoms. Found 48 (48 requested) and removed 24 (48 requested) atoms. Cycle 45: After refmac, R = 0.2184 (Rfree = 0.000) for 3272 atoms. Found 48 (48 requested) and removed 25 (48 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.61 2.41 NCS extension: 0 residues added, 3298 seeds are put forward Round 1: 210 peptides, 3 chains. Longest chain 151 peptides. Score 0.897 Round 2: 209 peptides, 4 chains. Longest chain 99 peptides. Score 0.888 Round 3: 211 peptides, 4 chains. Longest chain 112 peptides. Score 0.891 Round 4: 211 peptides, 3 chains. Longest chain 151 peptides. Score 0.898 Round 5: 208 peptides, 8 chains. Longest chain 47 peptides. Score 0.853 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 208, Estimated correctness of the model 98.7 % 3 chains (203 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 166 A and 171 A Built loop between residues 204 A and 209 A 2 chains (215 residues) following loop building 1 chains (211 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 20012 reflections ( 99.81 % complete ) and 1780 restraints for refining 1737 atoms. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2840 (Rfree = 0.000) for 1737 atoms. Found 25 (25 requested) and removed 0 (25 requested) atoms. Cycle 47: After refmac, R = 0.2557 (Rfree = 0.000) for 1737 atoms. Found 25 (26 requested) and removed 0 (26 requested) atoms. Cycle 48: After refmac, R = 0.2376 (Rfree = 0.000) for 1737 atoms. Found 23 (26 requested) and removed 0 (26 requested) atoms. Cycle 49: After refmac, R = 0.2251 (Rfree = 0.000) for 1737 atoms. Found 6 (26 requested) and removed 4 (26 requested) atoms. Writing output files ... TimeTaking 60.17