Mon 24 Dec 00:09:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl4-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:09:40 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 752 and 0 Target number of residues in the AU: 752 Target solvent content: 0.6045 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7152 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: 79.862 3.200 Wilson plot Bfac: 54.38 17516 reflections ( 99.52 % complete ) and 0 restraints for refining 7872 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3037 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2731 (Rfree = 0.000) for 7872 atoms. Found 70 (70 requested) and removed 83 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 7974 seeds are put forward NCS extension: 0 residues added, 7974 seeds are put forward Round 1: 534 peptides, 83 chains. Longest chain 20 peptides. Score 0.495 Round 2: 644 peptides, 68 chains. Longest chain 29 peptides. Score 0.697 Round 3: 668 peptides, 60 chains. Longest chain 36 peptides. Score 0.749 Round 4: 687 peptides, 60 chains. Longest chain 44 peptides. Score 0.763 Round 5: 709 peptides, 52 chains. Longest chain 44 peptides. Score 0.805 Taking the results from Round 5 Chains 59, Residues 657, Estimated correctness of the model 84.2 % 13 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 310 B and 315 B 58 chains (655 residues) following loop building 12 chains (294 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 10765 restraints for refining 6524 atoms. 7189 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2863 (Rfree = 0.000) for 6524 atoms. Found 58 (58 requested) and removed 81 (29 requested) atoms. Cycle 2: After refmac, R = 0.2604 (Rfree = 0.000) for 6416 atoms. Found 38 (57 requested) and removed 68 (29 requested) atoms. Cycle 3: After refmac, R = 0.2452 (Rfree = 0.000) for 6337 atoms. Found 28 (55 requested) and removed 45 (28 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2360 (Rfree = 0.000) for 6304 atoms. Found 15 (53 requested) and removed 42 (28 requested) atoms. Cycle 5: After refmac, R = 0.2293 (Rfree = 0.000) for 6264 atoms. Found 23 (52 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 6429 seeds are put forward NCS extension: 32 residues added (28 deleted due to clashes), 6461 seeds are put forward Round 1: 633 peptides, 67 chains. Longest chain 31 peptides. Score 0.691 Round 2: 679 peptides, 59 chains. Longest chain 47 peptides. Score 0.761 Round 3: 693 peptides, 55 chains. Longest chain 53 peptides. Score 0.785 Round 4: 668 peptides, 55 chains. Longest chain 54 peptides. Score 0.767 Round 5: 688 peptides, 58 chains. Longest chain 48 peptides. Score 0.771 Taking the results from Round 3 Chains 61, Residues 638, Estimated correctness of the model 81.1 % 10 chains (249 residues) have been docked in sequence Building loops using Loopy2018 61 chains (638 residues) following loop building 10 chains (249 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11177 restraints for refining 6529 atoms. 7708 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2608 (Rfree = 0.000) for 6529 atoms. Found 52 (52 requested) and removed 59 (29 requested) atoms. Cycle 7: After refmac, R = 0.2312 (Rfree = 0.000) for 6469 atoms. Found 27 (51 requested) and removed 43 (29 requested) atoms. Cycle 8: After refmac, R = 0.2166 (Rfree = 0.000) for 6429 atoms. Found 19 (49 requested) and removed 36 (28 requested) atoms. Cycle 9: After refmac, R = 0.2070 (Rfree = 0.000) for 6394 atoms. Found 13 (48 requested) and removed 30 (28 requested) atoms. Cycle 10: After refmac, R = 0.2015 (Rfree = 0.000) for 6364 atoms. Found 8 (47 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 6513 seeds are put forward NCS extension: 52 residues added (7 deleted due to clashes), 6565 seeds are put forward Round 1: 643 peptides, 67 chains. Longest chain 37 peptides. Score 0.700 Round 2: 667 peptides, 59 chains. Longest chain 61 peptides. Score 0.752 Round 3: 666 peptides, 53 chains. Longest chain 45 peptides. Score 0.773 Round 4: 676 peptides, 63 chains. Longest chain 36 peptides. Score 0.744 Round 5: 647 peptides, 58 chains. Longest chain 39 peptides. Score 0.740 Taking the results from Round 3 Chains 60, Residues 613, Estimated correctness of the model 79.1 % 12 chains (256 residues) have been docked in sequence Building loops using Loopy2018 60 chains (613 residues) following loop building 12 chains (256 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11265 restraints for refining 6529 atoms. 7880 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2465 (Rfree = 0.000) for 6529 atoms. Found 43 (46 requested) and removed 73 (29 requested) atoms. Cycle 12: After refmac, R = 0.2247 (Rfree = 0.000) for 6469 atoms. Found 20 (45 requested) and removed 45 (29 requested) atoms. Cycle 13: After refmac, R = 0.2121 (Rfree = 0.000) for 6431 atoms. Found 10 (43 requested) and removed 31 (28 requested) atoms. Cycle 14: After refmac, R = 0.2092 (Rfree = 0.000) for 6407 atoms. Found 13 (42 requested) and removed 29 (28 requested) atoms. Cycle 15: After refmac, R = 0.2043 (Rfree = 0.000) for 6379 atoms. Found 8 (41 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 2.92 Search for helices and strands: 0 residues in 0 chains, 6518 seeds are put forward NCS extension: 28 residues added (28 deleted due to clashes), 6546 seeds are put forward Round 1: 643 peptides, 65 chains. Longest chain 35 peptides. Score 0.709 Round 2: 657 peptides, 55 chains. Longest chain 35 peptides. Score 0.759 Round 3: 660 peptides, 64 chains. Longest chain 31 peptides. Score 0.727 Round 4: 663 peptides, 62 chains. Longest chain 24 peptides. Score 0.738 Round 5: 660 peptides, 53 chains. Longest chain 40 peptides. Score 0.769 Taking the results from Round 5 Chains 63, Residues 607, Estimated correctness of the model 78.4 % 13 chains (223 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 355 A and 364 A 63 chains (608 residues) following loop building 11 chains (231 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11519 restraints for refining 6529 atoms. 8436 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2697 (Rfree = 0.000) for 6529 atoms. Found 41 (41 requested) and removed 74 (29 requested) atoms. Cycle 17: After refmac, R = 0.2478 (Rfree = 0.000) for 6467 atoms. Found 39 (39 requested) and removed 48 (29 requested) atoms. Cycle 18: After refmac, R = 0.2320 (Rfree = 0.000) for 6441 atoms. Found 24 (38 requested) and removed 45 (28 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2222 (Rfree = 0.000) for 6413 atoms. Found 17 (36 requested) and removed 32 (28 requested) atoms. Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 6394 atoms. Found 19 (35 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 6587 seeds are put forward NCS extension: 39 residues added (30 deleted due to clashes), 6626 seeds are put forward Round 1: 587 peptides, 71 chains. Longest chain 27 peptides. Score 0.626 Round 2: 628 peptides, 57 chains. Longest chain 38 peptides. Score 0.729 Round 3: 657 peptides, 64 chains. Longest chain 35 peptides. Score 0.725 Round 4: 636 peptides, 59 chains. Longest chain 51 peptides. Score 0.727 Round 5: 636 peptides, 70 chains. Longest chain 28 peptides. Score 0.681 Taking the results from Round 2 Chains 62, Residues 571, Estimated correctness of the model 71.1 % 13 chains (243 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 124 A 59 chains (572 residues) following loop building 12 chains (249 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11364 restraints for refining 6529 atoms. 8243 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2575 (Rfree = 0.000) for 6529 atoms. Found 35 (35 requested) and removed 64 (29 requested) atoms. Cycle 22: After refmac, R = 0.2419 (Rfree = 0.000) for 6464 atoms. Found 29 (34 requested) and removed 35 (29 requested) atoms. Cycle 23: After refmac, R = 0.2531 (Rfree = 0.000) for 6440 atoms. Found 32 (32 requested) and removed 42 (28 requested) atoms. Cycle 24: After refmac, R = 0.2233 (Rfree = 0.000) for 6417 atoms. Found 15 (31 requested) and removed 31 (28 requested) atoms. Cycle 25: After refmac, R = 0.2430 (Rfree = 0.000) for 6392 atoms. Found 21 (30 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.87 Search for helices and strands: 0 residues in 0 chains, 6579 seeds are put forward NCS extension: 39 residues added (13 deleted due to clashes), 6618 seeds are put forward Round 1: 558 peptides, 64 chains. Longest chain 40 peptides. Score 0.629 Round 2: 607 peptides, 62 chains. Longest chain 28 peptides. Score 0.689 Round 3: 606 peptides, 57 chains. Longest chain 39 peptides. Score 0.710 Round 4: 623 peptides, 62 chains. Longest chain 37 peptides. Score 0.704 Round 5: 617 peptides, 62 chains. Longest chain 27 peptides. Score 0.698 Taking the results from Round 3 Chains 62, Residues 549, Estimated correctness of the model 67.3 % 11 chains (193 residues) have been docked in sequence Building loops using Loopy2018 62 chains (549 residues) following loop building 11 chains (193 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 12228 restraints for refining 6529 atoms. 9362 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2500 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 49 (29 requested) atoms. Cycle 27: After refmac, R = 0.2384 (Rfree = 0.000) for 6483 atoms. Found 24 (29 requested) and removed 38 (29 requested) atoms. Cycle 28: After refmac, R = 0.2258 (Rfree = 0.000) for 6457 atoms. Found 19 (29 requested) and removed 31 (29 requested) atoms. Cycle 29: After refmac, R = 0.2188 (Rfree = 0.000) for 6431 atoms. Found 16 (28 requested) and removed 28 (28 requested) atoms. Cycle 30: After refmac, R = 0.2144 (Rfree = 0.000) for 6413 atoms. Found 9 (28 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 6550 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6573 seeds are put forward Round 1: 542 peptides, 70 chains. Longest chain 26 peptides. Score 0.580 Round 2: 585 peptides, 59 chains. Longest chain 33 peptides. Score 0.681 Round 3: 593 peptides, 56 chains. Longest chain 45 peptides. Score 0.702 Round 4: 585 peptides, 62 chains. Longest chain 24 peptides. Score 0.667 Round 5: 601 peptides, 63 chains. Longest chain 27 peptides. Score 0.679 Taking the results from Round 3 Chains 61, Residues 537, Estimated correctness of the model 65.6 % 10 chains (195 residues) have been docked in sequence Building loops using Loopy2018 61 chains (537 residues) following loop building 10 chains (195 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 12139 restraints for refining 6529 atoms. 9337 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2450 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 53 (29 requested) atoms. Cycle 32: After refmac, R = 0.2371 (Rfree = 0.000) for 6489 atoms. Found 25 (29 requested) and removed 40 (29 requested) atoms. Cycle 33: After refmac, R = 0.2312 (Rfree = 0.000) for 6465 atoms. Found 22 (29 requested) and removed 31 (29 requested) atoms. Cycle 34: After refmac, R = 0.2263 (Rfree = 0.000) for 6450 atoms. Found 13 (28 requested) and removed 29 (28 requested) atoms. Cycle 35: After refmac, R = 0.2227 (Rfree = 0.000) for 6428 atoms. Found 19 (28 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 2.90 Search for helices and strands: 0 residues in 0 chains, 6580 seeds are put forward NCS extension: 34 residues added (19 deleted due to clashes), 6614 seeds are put forward Round 1: 526 peptides, 71 chains. Longest chain 36 peptides. Score 0.554 Round 2: 578 peptides, 61 chains. Longest chain 34 peptides. Score 0.665 Round 3: 586 peptides, 63 chains. Longest chain 36 peptides. Score 0.664 Round 4: 571 peptides, 65 chains. Longest chain 25 peptides. Score 0.638 Round 5: 586 peptides, 66 chains. Longest chain 41 peptides. Score 0.650 Taking the results from Round 2 Chains 71, Residues 517, Estimated correctness of the model 57.4 % 13 chains (183 residues) have been docked in sequence ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 12325 restraints for refining 6528 atoms. 9609 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2359 (Rfree = 0.000) for 6528 atoms. Found 29 (29 requested) and removed 45 (29 requested) atoms. Cycle 37: After refmac, R = 0.2252 (Rfree = 0.000) for 6497 atoms. Found 18 (29 requested) and removed 36 (29 requested) atoms. Cycle 38: After refmac, R = 0.2197 (Rfree = 0.000) for 6468 atoms. Found 13 (29 requested) and removed 32 (29 requested) atoms. Cycle 39: After refmac, R = 0.2178 (Rfree = 0.000) for 6443 atoms. Found 14 (28 requested) and removed 29 (28 requested) atoms. Cycle 40: After refmac, R = 0.2115 (Rfree = 0.000) for 6412 atoms. Found 9 (28 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 33 residues added (7 deleted due to clashes), 6576 seeds are put forward Round 1: 483 peptides, 60 chains. Longest chain 26 peptides. Score 0.563 Round 2: 518 peptides, 60 chains. Longest chain 30 peptides. Score 0.605 Round 3: 534 peptides, 66 chains. Longest chain 21 peptides. Score 0.592 Round 4: 542 peptides, 60 chains. Longest chain 43 peptides. Score 0.632 Round 5: 531 peptides, 61 chains. Longest chain 27 peptides. Score 0.615 Taking the results from Round 4 Chains 67, Residues 482, Estimated correctness of the model 49.4 % 11 chains (129 residues) have been docked in sequence ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 13004 restraints for refining 6529 atoms. 10650 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2385 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 42 (29 requested) atoms. Cycle 42: After refmac, R = 0.2279 (Rfree = 0.000) for 6496 atoms. Found 18 (29 requested) and removed 37 (29 requested) atoms. Cycle 43: After refmac, R = 0.2236 (Rfree = 0.000) for 6469 atoms. Found 25 (29 requested) and removed 31 (29 requested) atoms. Cycle 44: After refmac, R = 0.2224 (Rfree = 0.000) for 6453 atoms. Found 29 (29 requested) and removed 32 (29 requested) atoms. Cycle 45: After refmac, R = 0.2042 (Rfree = 0.000) for 6440 atoms. Found 11 (28 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 6585 seeds are put forward NCS extension: 53 residues added (5 deleted due to clashes), 6638 seeds are put forward Round 1: 464 peptides, 66 chains. Longest chain 22 peptides. Score 0.502 Round 2: 515 peptides, 62 chains. Longest chain 25 peptides. Score 0.591 Round 3: 515 peptides, 60 chains. Longest chain 32 peptides. Score 0.602 Round 4: 495 peptides, 63 chains. Longest chain 25 peptides. Score 0.561 Round 5: 508 peptides, 64 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 455, Estimated correctness of the model 41.6 % 7 chains (94 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 14 A and 23 A 62 chains (457 residues) following loop building 6 chains (102 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17516 reflections ( 99.52 % complete ) and 13343 restraints for refining 6528 atoms. 11180 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2410 (Rfree = 0.000) for 6528 atoms. Found 0 (29 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2321 (Rfree = 0.000) for 6478 atoms. Found 0 (29 requested) and removed 22 (29 requested) atoms. Cycle 48: After refmac, R = 0.2293 (Rfree = 0.000) for 6449 atoms. Found 0 (28 requested) and removed 26 (28 requested) atoms. Cycle 49: After refmac, R = 0.2367 (Rfree = 0.000) for 6416 atoms. TimeTaking 68.17