Mon 24 Dec 08:04:11 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 1vp7-3.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.0-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/1vp7-3.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.0-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 08:04:15 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/1vp7-3.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.0-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 625 and 0 Target number of residues in the AU: 625 Target solvent content: 0.5057 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.0-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 4800 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: 207.138 3.000 Wilson plot Bfac: 24.67 14741 reflections ( 99.77 % complete ) and 0 restraints for refining 5289 atoms. Observations/parameters ratio is 0.70 ------------------------------------------------------ Starting model: R = 0.3233 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3041 (Rfree = 0.000) for 5289 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.56 2.46 Search for helices and strands: 0 residues in 0 chains, 5395 seeds are put forward NCS extension: 0 residues added, 5395 seeds are put forward Round 1: 262 peptides, 35 chains. Longest chain 22 peptides. Score 0.488 Round 2: 314 peptides, 33 chains. Longest chain 40 peptides. Score 0.608 Round 3: 327 peptides, 39 chains. Longest chain 41 peptides. Score 0.581 Round 4: 334 peptides, 32 chains. Longest chain 46 peptides. Score 0.650 Round 5: 340 peptides, 35 chains. Longest chain 42 peptides. Score 0.636 Taking the results from Round 4 Chains 33, Residues 302, Estimated correctness of the model 62.3 % 6 chains (138 residues) have been docked in sequence ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 7654 restraints for refining 4349 atoms. 5944 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2945 (Rfree = 0.000) for 4349 atoms. Found 47 (47 requested) and removed 63 (23 requested) atoms. Cycle 2: After refmac, R = 0.2865 (Rfree = 0.000) for 4242 atoms. Found 42 (46 requested) and removed 49 (23 requested) atoms. Cycle 3: After refmac, R = 0.2748 (Rfree = 0.000) for 4190 atoms. Found 38 (45 requested) and removed 28 (22 requested) atoms. Cycle 4: After refmac, R = 0.2655 (Rfree = 0.000) for 4157 atoms. Found 35 (45 requested) and removed 33 (22 requested) atoms. Cycle 5: After refmac, R = 0.2666 (Rfree = 0.000) for 4143 atoms. Found 30 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.42 2.33 Search for helices and strands: 0 residues in 0 chains, 4273 seeds are put forward NCS extension: 0 residues added, 4273 seeds are put forward Round 1: 330 peptides, 33 chains. Longest chain 33 peptides. Score 0.635 Round 2: 342 peptides, 27 chains. Longest chain 34 peptides. Score 0.698 Round 3: 339 peptides, 30 chains. Longest chain 40 peptides. Score 0.672 Round 4: 350 peptides, 32 chains. Longest chain 32 peptides. Score 0.674 Round 5: 344 peptides, 28 chains. Longest chain 33 peptides. Score 0.694 Taking the results from Round 2 Chains 34, Residues 315, Estimated correctness of the model 71.2 % 10 chains (207 residues) have been docked in sequence ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6614 restraints for refining 4256 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2817 (Rfree = 0.000) for 4256 atoms. Found 46 (46 requested) and removed 62 (23 requested) atoms. Cycle 7: After refmac, R = 0.2642 (Rfree = 0.000) for 4209 atoms. Found 35 (45 requested) and removed 35 (22 requested) atoms. Cycle 8: After refmac, R = 0.2527 (Rfree = 0.000) for 4201 atoms. Found 23 (45 requested) and removed 28 (22 requested) atoms. Cycle 9: After refmac, R = 0.2577 (Rfree = 0.000) for 4183 atoms. Found 25 (45 requested) and removed 28 (22 requested) atoms. Cycle 10: After refmac, R = 0.2408 (Rfree = 0.000) for 4171 atoms. Found 23 (45 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.43 2.33 Search for helices and strands: 0 residues in 0 chains, 4321 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 4331 seeds are put forward Round 1: 336 peptides, 25 chains. Longest chain 51 peptides. Score 0.704 Round 2: 337 peptides, 27 chains. Longest chain 27 peptides. Score 0.691 Round 3: 353 peptides, 28 chains. Longest chain 31 peptides. Score 0.707 Round 4: 359 peptides, 30 chains. Longest chain 36 peptides. Score 0.702 Round 5: 349 peptides, 29 chains. Longest chain 52 peptides. Score 0.694 Taking the results from Round 3 Chains 30, Residues 325, Estimated correctness of the model 72.8 % 10 chains (208 residues) have been docked in sequence Building loops using Loopy2018 30 chains (325 residues) following loop building 10 chains (208 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6432 restraints for refining 4242 atoms. 4339 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2717 (Rfree = 0.000) for 4242 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 12: After refmac, R = 0.2517 (Rfree = 0.000) for 4222 atoms. Found 21 (44 requested) and removed 35 (22 requested) atoms. Cycle 13: After refmac, R = 0.2418 (Rfree = 0.000) for 4194 atoms. Found 21 (43 requested) and removed 29 (22 requested) atoms. Cycle 14: After refmac, R = 0.2360 (Rfree = 0.000) for 4171 atoms. Found 20 (42 requested) and removed 25 (22 requested) atoms. Cycle 15: After refmac, R = 0.2299 (Rfree = 0.000) for 4151 atoms. Found 9 (40 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.50 2.40 Search for helices and strands: 0 residues in 0 chains, 4252 seeds are put forward NCS extension: 5 residues added (2 deleted due to clashes), 4257 seeds are put forward Round 1: 339 peptides, 23 chains. Longest chain 51 peptides. Score 0.722 Round 2: 345 peptides, 26 chains. Longest chain 46 peptides. Score 0.710 Round 3: 338 peptides, 27 chains. Longest chain 51 peptides. Score 0.693 Round 4: 338 peptides, 30 chains. Longest chain 27 peptides. Score 0.671 Round 5: 337 peptides, 29 chains. Longest chain 39 peptides. Score 0.677 Taking the results from Round 1 Chains 28, Residues 316, Estimated correctness of the model 75.3 % 11 chains (208 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 C and 43 C Built loop between residues 33 B and 37 B Built loop between residues 51 B and 57 B 24 chains (323 residues) following loop building 8 chains (218 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6275 restraints for refining 4195 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2584 (Rfree = 0.000) for 4195 atoms. Found 40 (40 requested) and removed 44 (22 requested) atoms. Cycle 17: After refmac, R = 0.2466 (Rfree = 0.000) for 4182 atoms. Found 24 (40 requested) and removed 24 (22 requested) atoms. Cycle 18: After refmac, R = 0.2379 (Rfree = 0.000) for 4173 atoms. Found 10 (39 requested) and removed 23 (22 requested) atoms. Cycle 19: After refmac, R = 0.2316 (Rfree = 0.000) for 4150 atoms. Found 9 (37 requested) and removed 23 (22 requested) atoms. Cycle 20: After refmac, R = 0.2282 (Rfree = 0.000) for 4128 atoms. Found 17 (36 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.44 2.34 Search for helices and strands: 0 residues in 0 chains, 4261 seeds are put forward NCS extension: 13 residues added (11 deleted due to clashes), 4274 seeds are put forward Round 1: 319 peptides, 26 chains. Longest chain 51 peptides. Score 0.672 Round 2: 338 peptides, 22 chains. Longest chain 43 peptides. Score 0.727 Round 3: 337 peptides, 25 chains. Longest chain 53 peptides. Score 0.705 Round 4: 341 peptides, 22 chains. Longest chain 65 peptides. Score 0.731 Round 5: 343 peptides, 28 chains. Longest chain 39 peptides. Score 0.693 Taking the results from Round 4 Chains 24, Residues 319, Estimated correctness of the model 76.7 % 6 chains (176 residues) have been docked in sequence Building loops using Loopy2018 24 chains (319 residues) following loop building 6 chains (176 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6802 restraints for refining 4187 atoms. 4881 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2687 (Rfree = 0.000) for 4187 atoms. Found 36 (36 requested) and removed 49 (22 requested) atoms. Cycle 22: After refmac, R = 0.2604 (Rfree = 0.000) for 4164 atoms. Found 35 (35 requested) and removed 28 (22 requested) atoms. Cycle 23: After refmac, R = 0.2449 (Rfree = 0.000) for 4158 atoms. Found 27 (33 requested) and removed 24 (22 requested) atoms. Cycle 24: After refmac, R = 0.2408 (Rfree = 0.000) for 4154 atoms. Found 21 (33 requested) and removed 23 (22 requested) atoms. Cycle 25: After refmac, R = 0.2423 (Rfree = 0.000) for 4143 atoms. Found 18 (32 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.44 2.34 Search for helices and strands: 0 residues in 0 chains, 4257 seeds are put forward NCS extension: 9 residues added (10 deleted due to clashes), 4266 seeds are put forward Round 1: 320 peptides, 24 chains. Longest chain 51 peptides. Score 0.688 Round 2: 335 peptides, 23 chains. Longest chain 64 peptides. Score 0.717 Round 3: 331 peptides, 26 chains. Longest chain 51 peptides. Score 0.690 Round 4: 336 peptides, 28 chains. Longest chain 36 peptides. Score 0.683 Round 5: 337 peptides, 24 chains. Longest chain 51 peptides. Score 0.712 Taking the results from Round 2 Chains 23, Residues 312, Estimated correctness of the model 74.5 % 7 chains (184 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 B and 62 B 22 chains (314 residues) following loop building 6 chains (186 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6519 restraints for refining 4174 atoms. 4569 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2615 (Rfree = 0.000) for 4174 atoms. Found 31 (31 requested) and removed 36 (22 requested) atoms. Cycle 27: After refmac, R = 0.2496 (Rfree = 0.000) for 4161 atoms. Found 23 (30 requested) and removed 30 (22 requested) atoms. Cycle 28: After refmac, R = 0.2424 (Rfree = 0.000) for 4144 atoms. Found 21 (29 requested) and removed 26 (22 requested) atoms. Cycle 29: After refmac, R = 0.2321 (Rfree = 0.000) for 4123 atoms. Found 19 (28 requested) and removed 25 (22 requested) atoms. Cycle 30: After refmac, R = 0.2298 (Rfree = 0.000) for 4110 atoms. Found 17 (27 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.47 2.37 Search for helices and strands: 0 residues in 0 chains, 4214 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 4221 seeds are put forward Round 1: 329 peptides, 28 chains. Longest chain 40 peptides. Score 0.672 Round 2: 333 peptides, 24 chains. Longest chain 52 peptides. Score 0.707 Round 3: 342 peptides, 25 chains. Longest chain 52 peptides. Score 0.712 Round 4: 345 peptides, 25 chains. Longest chain 33 peptides. Score 0.716 Round 5: 342 peptides, 24 chains. Longest chain 55 peptides. Score 0.719 Taking the results from Round 5 Chains 24, Residues 318, Estimated correctness of the model 74.8 % 7 chains (205 residues) have been docked in sequence Building loops using Loopy2018 24 chains (318 residues) following loop building 7 chains (205 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6425 restraints for refining 4208 atoms. 4376 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2653 (Rfree = 0.000) for 4208 atoms. Found 27 (27 requested) and removed 51 (22 requested) atoms. Cycle 32: After refmac, R = 0.2510 (Rfree = 0.000) for 4168 atoms. Found 26 (26 requested) and removed 25 (22 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2438 (Rfree = 0.000) for 4159 atoms. Found 24 (25 requested) and removed 23 (22 requested) atoms. Cycle 34: After refmac, R = 0.2377 (Rfree = 0.000) for 4153 atoms. Found 10 (24 requested) and removed 23 (22 requested) atoms. Cycle 35: After refmac, R = 0.2311 (Rfree = 0.000) for 4128 atoms. Found 13 (23 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.48 2.38 Search for helices and strands: 0 residues in 0 chains, 4230 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4243 seeds are put forward Round 1: 339 peptides, 28 chains. Longest chain 32 peptides. Score 0.687 Round 2: 351 peptides, 25 chains. Longest chain 56 peptides. Score 0.725 Round 3: 350 peptides, 26 chains. Longest chain 69 peptides. Score 0.716 Round 4: 336 peptides, 26 chains. Longest chain 35 peptides. Score 0.697 Round 5: 343 peptides, 30 chains. Longest chain 31 peptides. Score 0.678 Taking the results from Round 2 Chains 29, Residues 326, Estimated correctness of the model 75.8 % 7 chains (176 residues) have been docked in sequence Building loops using Loopy2018 29 chains (326 residues) following loop building 7 chains (176 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6625 restraints for refining 4166 atoms. 4679 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2682 (Rfree = 0.000) for 4166 atoms. Found 22 (22 requested) and removed 47 (22 requested) atoms. Cycle 37: After refmac, R = 0.2420 (Rfree = 0.000) for 4126 atoms. Found 22 (22 requested) and removed 24 (22 requested) atoms. Cycle 38: After refmac, R = 0.2328 (Rfree = 0.000) for 4108 atoms. Found 9 (22 requested) and removed 23 (22 requested) atoms. Cycle 39: After refmac, R = 0.2288 (Rfree = 0.000) for 4086 atoms. Found 8 (22 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2256 (Rfree = 0.000) for 4068 atoms. Found 12 (21 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.48 2.38 Search for helices and strands: 0 residues in 0 chains, 4177 seeds are put forward NCS extension: 24 residues added (39 deleted due to clashes), 4201 seeds are put forward Round 1: 313 peptides, 25 chains. Longest chain 31 peptides. Score 0.670 Round 2: 336 peptides, 23 chains. Longest chain 34 peptides. Score 0.718 Round 3: 326 peptides, 23 chains. Longest chain 51 peptides. Score 0.704 Round 4: 339 peptides, 23 chains. Longest chain 39 peptides. Score 0.722 Round 5: 344 peptides, 26 chains. Longest chain 28 peptides. Score 0.708 Taking the results from Round 4 Chains 24, Residues 316, Estimated correctness of the model 75.3 % 10 chains (220 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 C and 79 C Built loop between residues 51 D and 55 D 22 chains (320 residues) following loop building 8 chains (225 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 5949 restraints for refining 4152 atoms. 3827 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 4152 atoms. Found 22 (22 requested) and removed 43 (22 requested) atoms. Cycle 42: After refmac, R = 0.2441 (Rfree = 0.000) for 4120 atoms. Found 22 (22 requested) and removed 24 (22 requested) atoms. Cycle 43: After refmac, R = 0.2481 (Rfree = 0.000) for 4109 atoms. Found 22 (22 requested) and removed 25 (22 requested) atoms. Cycle 44: After refmac, R = 0.2259 (Rfree = 0.000) for 4099 atoms. Found 18 (22 requested) and removed 27 (22 requested) atoms. Cycle 45: After refmac, R = 0.2203 (Rfree = 0.000) for 4078 atoms. Found 13 (22 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.49 2.39 Search for helices and strands: 0 residues in 0 chains, 4193 seeds are put forward NCS extension: 42 residues added (49 deleted due to clashes), 4235 seeds are put forward Round 1: 316 peptides, 24 chains. Longest chain 31 peptides. Score 0.682 Round 2: 329 peptides, 23 chains. Longest chain 35 peptides. Score 0.708 Round 3: 324 peptides, 20 chains. Longest chain 63 peptides. Score 0.722 Round 4: 314 peptides, 22 chains. Longest chain 39 peptides. Score 0.694 Round 5: 316 peptides, 22 chains. Longest chain 30 peptides. Score 0.697 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 304, Estimated correctness of the model 75.3 % 6 chains (176 residues) have been docked in sequence Sequence coverage is 57 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 44 A and 55 A 21 chains (313 residues) following loop building 5 chains (186 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14741 reflections ( 99.77 % complete ) and 6324 restraints for refining 4112 atoms. 4426 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2595 (Rfree = 0.000) for 4112 atoms. Found 0 (22 requested) and removed 6 (22 requested) atoms. Cycle 47: After refmac, R = 0.2475 (Rfree = 0.000) for 4096 atoms. Found 0 (22 requested) and removed 3 (22 requested) atoms. Cycle 48: After refmac, R = 0.2476 (Rfree = 0.000) for 4085 atoms. Found 0 (22 requested) and removed 7 (22 requested) atoms. Cycle 49: After refmac, R = 0.2417 (Rfree = 0.000) for 4072 atoms. TimeTaking 71.13