Mon 24 Dec 01:09:05 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 1vlm-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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/1vlm-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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 01:09:10 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/1vlm-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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 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-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.50 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 3914 atoms. Observations/parameters ratio is 1.44 ------------------------------------------------------ Starting model: R = 0.3285 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2785 (Rfree = 0.000) for 3914 atoms. Found 102 (102 requested) and removed 51 (51 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 3965 seeds are put forward Round 1: 260 peptides, 37 chains. Longest chain 25 peptides. Score 0.573 Round 2: 301 peptides, 28 chains. Longest chain 39 peptides. Score 0.759 Round 3: 333 peptides, 21 chains. Longest chain 67 peptides. Score 0.852 Round 4: 348 peptides, 22 chains. Longest chain 50 peptides. Score 0.862 Round 5: 362 peptides, 15 chains. Longest chain 120 peptides. Score 0.908 Taking the results from Round 5 Chains 17, Residues 347, Estimated correctness of the model 98.8 % 8 chains (277 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 53 A Built loop between residues 118 A and 126 A Built loop between residues 187 A and 191 A 12 chains (358 residues) following loop building 5 chains (291 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 4215 restraints for refining 3485 atoms. 1610 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3089 (Rfree = 0.000) for 3485 atoms. Found 83 (90 requested) and removed 53 (45 requested) atoms. Cycle 2: After refmac, R = 0.2822 (Rfree = 0.000) for 3488 atoms. Found 63 (89 requested) and removed 46 (45 requested) atoms. Cycle 3: After refmac, R = 0.2655 (Rfree = 0.000) for 3479 atoms. Found 56 (87 requested) and removed 46 (45 requested) atoms. Cycle 4: After refmac, R = 0.2529 (Rfree = 0.000) for 3476 atoms. Found 37 (86 requested) and removed 45 (45 requested) atoms. Cycle 5: After refmac, R = 0.2453 (Rfree = 0.000) for 3462 atoms. Found 42 (83 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.29 2.42 NCS extension: 67 residues added (200 deleted due to clashes), 3530 seeds are put forward Round 1: 376 peptides, 11 chains. Longest chain 132 peptides. Score 0.932 Round 2: 379 peptides, 9 chains. Longest chain 142 peptides. Score 0.940 Round 3: 384 peptides, 6 chains. Longest chain 132 peptides. Score 0.952 Round 4: 380 peptides, 9 chains. Longest chain 121 peptides. Score 0.941 Round 5: 371 peptides, 9 chains. Longest chain 85 peptides. Score 0.936 Taking the results from Round 3 Chains 8, Residues 378, Estimated correctness of the model 99.6 % 5 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 B and 93 B 7 chains (380 residues) following loop building 4 chains (363 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3733 restraints for refining 3597 atoms. 645 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2719 (Rfree = 0.000) for 3597 atoms. Found 76 (84 requested) and removed 62 (46 requested) atoms. Cycle 7: After refmac, R = 0.2474 (Rfree = 0.000) for 3600 atoms. Found 61 (83 requested) and removed 47 (47 requested) atoms. Cycle 8: After refmac, R = 0.2353 (Rfree = 0.000) for 3602 atoms. Found 41 (81 requested) and removed 47 (47 requested) atoms. Cycle 9: After refmac, R = 0.2259 (Rfree = 0.000) for 3587 atoms. Found 39 (78 requested) and removed 46 (46 requested) atoms. Cycle 10: After refmac, R = 0.2201 (Rfree = 0.000) for 3572 atoms. Found 43 (76 requested) and removed 25 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.28 2.41 NCS extension: 121 residues added (186 deleted due to clashes), 3712 seeds are put forward Round 1: 387 peptides, 11 chains. Longest chain 131 peptides. Score 0.937 Round 2: 391 peptides, 10 chains. Longest chain 93 peptides. Score 0.942 Round 3: 383 peptides, 10 chains. Longest chain 144 peptides. Score 0.939 Round 4: 385 peptides, 9 chains. Longest chain 93 peptides. Score 0.943 Round 5: 388 peptides, 11 chains. Longest chain 93 peptides. Score 0.938 Taking the results from Round 4 Chains 9, Residues 376, Estimated correctness of the model 99.5 % 6 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 85 A Built loop between residues 176 A and 180 A Built loop between residues 90 B and 93 B 5 chains (387 residues) following loop building 3 chains (374 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3742 restraints for refining 3613 atoms. 605 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2571 (Rfree = 0.000) for 3613 atoms. Found 75 (75 requested) and removed 63 (47 requested) atoms. Cycle 12: After refmac, R = 0.2369 (Rfree = 0.000) for 3619 atoms. Found 55 (73 requested) and removed 47 (47 requested) atoms. Cycle 13: After refmac, R = 0.2264 (Rfree = 0.000) for 3624 atoms. Found 46 (71 requested) and removed 47 (47 requested) atoms. Cycle 14: After refmac, R = 0.2197 (Rfree = 0.000) for 3620 atoms. Found 44 (70 requested) and removed 40 (47 requested) atoms. Cycle 15: After refmac, R = 0.2127 (Rfree = 0.000) for 3622 atoms. Found 46 (68 requested) and removed 25 (47 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.27 2.39 NCS extension: 44 residues added (183 deleted due to clashes), 3691 seeds are put forward Round 1: 388 peptides, 9 chains. Longest chain 139 peptides. Score 0.944 Round 2: 395 peptides, 9 chains. Longest chain 135 peptides. Score 0.947 Round 3: 398 peptides, 7 chains. Longest chain 141 peptides. Score 0.954 Round 4: 396 peptides, 9 chains. Longest chain 125 peptides. Score 0.947 Round 5: 396 peptides, 9 chains. Longest chain 132 peptides. Score 0.947 Taking the results from Round 3 Chains 7, Residues 391, Estimated correctness of the model 99.7 % 5 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 58 A Built loop between residues 74 A and 85 A Built loop between residues 152 B and 159 B 3 chains (405 residues) following loop building 2 chains (401 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3636 restraints for refining 3682 atoms. 300 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2522 (Rfree = 0.000) for 3682 atoms. Found 67 (67 requested) and removed 55 (48 requested) atoms. Cycle 17: After refmac, R = 0.2330 (Rfree = 0.000) for 3682 atoms. Found 56 (65 requested) and removed 48 (48 requested) atoms. Cycle 18: After refmac, R = 0.2241 (Rfree = 0.000) for 3688 atoms. Found 57 (63 requested) and removed 48 (48 requested) atoms. Cycle 19: After refmac, R = 0.2198 (Rfree = 0.000) for 3697 atoms. Found 35 (61 requested) and removed 36 (48 requested) atoms. Cycle 20: After refmac, R = 0.2173 (Rfree = 0.000) for 3696 atoms. Found 40 (60 requested) and removed 41 (48 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.29 2.42 NCS extension: 37 residues added (170 deleted due to clashes), 3736 seeds are put forward Round 1: 396 peptides, 6 chains. Longest chain 141 peptides. Score 0.957 Round 2: 398 peptides, 7 chains. Longest chain 142 peptides. Score 0.954 Round 3: 396 peptides, 7 chains. Longest chain 140 peptides. Score 0.954 Round 4: 396 peptides, 8 chains. Longest chain 142 peptides. Score 0.951 Round 5: 397 peptides, 11 chains. Longest chain 98 peptides. Score 0.942 Taking the results from Round 1 Chains 6, Residues 390, Estimated correctness of the model 99.7 % 4 chains (383 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 84 A Built loop between residues 152 B and 160 B 3 chains (404 residues) following loop building 2 chains (400 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3625 restraints for refining 3709 atoms. 298 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2474 (Rfree = 0.000) for 3709 atoms. Found 58 (58 requested) and removed 53 (48 requested) atoms. Cycle 22: After refmac, R = 0.2280 (Rfree = 0.000) for 3705 atoms. Found 56 (56 requested) and removed 48 (48 requested) atoms. Cycle 23: After refmac, R = 0.2178 (Rfree = 0.000) for 3708 atoms. Found 53 (54 requested) and removed 48 (48 requested) atoms. Cycle 24: After refmac, R = 0.2109 (Rfree = 0.000) for 3710 atoms. Found 39 (52 requested) and removed 31 (48 requested) atoms. Cycle 25: After refmac, R = 0.2092 (Rfree = 0.000) for 3715 atoms. Found 37 (50 requested) and removed 37 (48 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.27 2.39 NCS extension: 34 residues added (184 deleted due to clashes), 3755 seeds are put forward Round 1: 395 peptides, 7 chains. Longest chain 139 peptides. Score 0.953 Round 2: 396 peptides, 7 chains. Longest chain 130 peptides. Score 0.954 Round 3: 396 peptides, 9 chains. Longest chain 135 peptides. Score 0.947 Round 4: 397 peptides, 10 chains. Longest chain 130 peptides. Score 0.945 Round 5: 392 peptides, 9 chains. Longest chain 130 peptides. Score 0.946 Taking the results from Round 2 Chains 7, Residues 389, Estimated correctness of the model 99.7 % 5 chains (377 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 78 A Built loop between residues 188 A and 191 A 5 chains (395 residues) following loop building 3 chains (383 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3746 restraints for refining 3680 atoms. 538 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2323 (Rfree = 0.000) for 3680 atoms. Found 48 (48 requested) and removed 53 (48 requested) atoms. Cycle 27: After refmac, R = 0.2176 (Rfree = 0.000) for 3671 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 28: After refmac, R = 0.2109 (Rfree = 0.000) for 3671 atoms. Found 43 (47 requested) and removed 47 (47 requested) atoms. Cycle 29: After refmac, R = 0.2075 (Rfree = 0.000) for 3664 atoms. Found 47 (47 requested) and removed 37 (47 requested) atoms. Cycle 30: After refmac, R = 0.2062 (Rfree = 0.000) for 3671 atoms. Found 44 (47 requested) and removed 38 (47 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.27 2.39 NCS extension: 47 residues added (244 deleted due to clashes), 3726 seeds are put forward Round 1: 398 peptides, 7 chains. Longest chain 143 peptides. Score 0.954 Round 2: 397 peptides, 7 chains. Longest chain 141 peptides. Score 0.954 Round 3: 398 peptides, 9 chains. Longest chain 125 peptides. Score 0.948 Round 4: 397 peptides, 8 chains. Longest chain 143 peptides. Score 0.951 Round 5: 393 peptides, 11 chains. Longest chain 124 peptides. Score 0.940 Taking the results from Round 2 Chains 7, Residues 390, Estimated correctness of the model 99.7 % 5 chains (384 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 83 A Built loop between residues 152 B and 159 B Built loop between residues 177 B and 180 B 3 chains (404 residues) following loop building 2 chains (401 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3575 restraints for refining 3673 atoms. 243 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2395 (Rfree = 0.000) for 3673 atoms. Found 47 (47 requested) and removed 56 (47 requested) atoms. Cycle 32: After refmac, R = 0.2224 (Rfree = 0.000) for 3660 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 33: After refmac, R = 0.2136 (Rfree = 0.000) for 3660 atoms. Found 43 (47 requested) and removed 48 (47 requested) atoms. Cycle 34: After refmac, R = 0.2096 (Rfree = 0.000) for 3652 atoms. Found 42 (47 requested) and removed 33 (47 requested) atoms. Cycle 35: After refmac, R = 0.2060 (Rfree = 0.000) for 3661 atoms. Found 32 (47 requested) and removed 34 (47 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.42 NCS extension: 46 residues added (172 deleted due to clashes), 3712 seeds are put forward Round 1: 396 peptides, 7 chains. Longest chain 98 peptides. Score 0.954 Round 2: 394 peptides, 9 chains. Longest chain 141 peptides. Score 0.947 Round 3: 396 peptides, 8 chains. Longest chain 111 peptides. Score 0.951 Round 4: 385 peptides, 10 chains. Longest chain 75 peptides. Score 0.940 Round 5: 395 peptides, 9 chains. Longest chain 136 peptides. Score 0.947 Taking the results from Round 1 Chains 11, Residues 389, Estimated correctness of the model 99.7 % 6 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 B and 112 B Built loop between residues 152 B and 160 B 9 chains (398 residues) following loop building 4 chains (372 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3702 restraints for refining 3620 atoms. 521 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2328 (Rfree = 0.000) for 3620 atoms. Found 47 (47 requested) and removed 50 (47 requested) atoms. Cycle 37: After refmac, R = 0.2182 (Rfree = 0.000) for 3612 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 38: After refmac, R = 0.2133 (Rfree = 0.000) for 3609 atoms. Found 31 (47 requested) and removed 47 (47 requested) atoms. Cycle 39: After refmac, R = 0.2086 (Rfree = 0.000) for 3593 atoms. Found 40 (46 requested) and removed 25 (46 requested) atoms. Cycle 40: After refmac, R = 0.2034 (Rfree = 0.000) for 3607 atoms. Found 30 (47 requested) and removed 31 (47 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.29 2.42 NCS extension: 112 residues added (546 deleted due to clashes), 3721 seeds are put forward Round 1: 394 peptides, 7 chains. Longest chain 140 peptides. Score 0.953 Round 2: 397 peptides, 6 chains. Longest chain 140 peptides. Score 0.957 Round 3: 389 peptides, 11 chains. Longest chain 125 peptides. Score 0.938 Round 4: 393 peptides, 9 chains. Longest chain 79 peptides. Score 0.946 Round 5: 388 peptides, 13 chains. Longest chain 93 peptides. Score 0.931 Taking the results from Round 2 Chains 6, Residues 391, Estimated correctness of the model 99.7 % 5 chains (387 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 79 A Built loop between residues 109 B and 112 B Built loop between residues 152 B and 159 B 3 chains (404 residues) following loop building 2 chains (400 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3579 restraints for refining 3655 atoms. 252 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2337 (Rfree = 0.000) for 3655 atoms. Found 47 (47 requested) and removed 53 (47 requested) atoms. Cycle 42: After refmac, R = 0.2204 (Rfree = 0.000) for 3642 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 43: After refmac, R = 0.2132 (Rfree = 0.000) for 3639 atoms. Found 37 (47 requested) and removed 47 (47 requested) atoms. Cycle 44: After refmac, R = 0.2097 (Rfree = 0.000) for 3626 atoms. Found 40 (47 requested) and removed 44 (47 requested) atoms. Cycle 45: After refmac, R = 0.2076 (Rfree = 0.000) for 3621 atoms. Found 47 (47 requested) and removed 31 (47 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.30 2.43 NCS extension: 5 residues added (6 deleted due to clashes), 3645 seeds are put forward Round 1: 395 peptides, 7 chains. Longest chain 140 peptides. Score 0.953 Round 2: 394 peptides, 8 chains. Longest chain 130 peptides. Score 0.950 Round 3: 394 peptides, 9 chains. Longest chain 142 peptides. Score 0.947 Round 4: 395 peptides, 9 chains. Longest chain 117 peptides. Score 0.947 Round 5: 388 peptides, 11 chains. Longest chain 108 peptides. Score 0.938 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 388, Estimated correctness of the model 99.6 % 6 chains (385 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 100 A and 103 A Built loop between residues 151 A and 159 A Built loop between residues 54 B and 57 B Built loop between residues 73 B and 79 B 3 chains (404 residues) following loop building 2 chains (401 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22604 reflections ( 98.93 % complete ) and 3332 restraints for refining 3264 atoms. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2672 (Rfree = 0.000) for 3264 atoms. Found 21 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2478 (Rfree = 0.000) for 3264 atoms. Found 9 (42 requested) and removed 1 (42 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2379 (Rfree = 0.000) for 3264 atoms. Found 4 (42 requested) and removed 0 (42 requested) atoms. Cycle 49: After refmac, R = 0.2326 (Rfree = 0.000) for 3264 atoms. TimeTaking 55